AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene83861

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene83861.t1 MTR_4g088015 66.667 54 17 1 121 174 220 272 2.98e-17 78.6
MS.gene83861.t1 MTR_3g463400 57.407 54 22 1 121 174 132 184 4.76e-15 72.4
MS.gene83861.t1 MTR_5g070020 57.407 54 22 1 121 174 121 173 1.16e-14 70.9
MS.gene83861.t1 MTR_5g049190 52.542 59 27 1 116 174 13 70 1.41e-14 69.7
MS.gene83861.t1 MTR_7g451170 57.407 54 22 1 121 174 190 242 2.47e-14 70.1
MS.gene83861.t1 MTR_7g037260 55.556 54 23 1 121 174 144 196 2.40e-13 67.0
MS.gene83861.t1 MTR_7g035350 52.727 55 25 1 120 174 223 276 2.67e-13 67.4
MS.gene83861.t1 MTR_3g077650 55.556 54 23 1 121 174 180 232 4.38e-13 66.6
MS.gene83861.t1 MTR_1g057980 56.364 55 22 2 121 174 78 131 8.46e-13 65.5
MS.gene83861.t1 MTR_4g105660 44.156 77 35 2 108 177 159 234 2.69e-12 64.3
MS.gene83861.t1 MTR_7g037130 51.852 54 25 1 121 174 144 196 2.41e-11 61.6
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene83861.t1 AT3G27785 58.621 58 23 1 117 174 184 240 1.28e-15 73.9
MS.gene83861.t1 AT5G58850 53.704 54 24 1 121 174 104 156 3.56e-14 69.7
MS.gene83861.t1 AT5G11050 55.556 54 23 1 121 174 104 156 3.84e-14 69.7
MS.gene83861.t1 AT4G18770 47.541 61 31 1 114 174 209 268 1.25e-13 68.2
MS.gene83861.t1 AT5G40360 50.769 65 30 2 111 174 146 209 8.03e-12 62.8

Find 36 sgRNAs with CRISPR-Local

Find 51 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ATATAGGGAACTTGTTAAAT+TGG 0.199609 6.1:+9586391 MS.gene83861:intron
TAGATGACTGTTTAAGATAT+TGG 0.217151 6.1:-9585982 None:intergenic
CGCTCCAAACATGGATATTC+TGG 0.220757 6.1:-9585843 None:intergenic
TTTAAGATATTGGGATTATT+AGG 0.225450 6.1:-9585972 None:intergenic
TCATCTCCGTCCAAACATTA+AGG 0.270772 6.1:+9586505 MS.gene83861:CDS
AGATGACTGTTTAAGATATT+GGG 0.311205 6.1:-9585981 None:intergenic
ATGATGACATGCCACGTAAA+TGG 0.337422 6.1:-9586025 None:intergenic
GGAACATAAACCTTAATGTT+TGG 0.342814 6.1:-9586515 None:intergenic
TTCATCAATCTTGCAATTTG+AGG 0.352946 6.1:-9586440 None:intergenic
GCATAAGCTTTGTTGACGTC+TGG 0.422118 6.1:-9586125 None:intergenic
CAAAACAGTGTCGTGATAGA+TGG 0.437524 6.1:+9586477 MS.gene83861:CDS
GAACGAGAATTGACCTTTGT+GGG 0.444047 6.1:-9585878 None:intergenic
AAATGGATGACATGCATGTT+TGG 0.446835 6.1:-9586008 None:intergenic
TTGTTGACGTCTGGTACAAA+TGG 0.468340 6.1:-9586116 None:intergenic
TATTAGGTACACTCAAGATA+TGG 0.470686 6.1:-9585956 None:intergenic
ACCATCTCGATGGAAACATC+TGG 0.493183 6.1:-9586081 None:intergenic
CTTATGCAATCAGAAAGAAA+TGG 0.496059 6.1:+9586141 MS.gene83861:CDS
CATAAACCTTAATGTTTGGA+CGG 0.508200 6.1:-9586511 None:intergenic
GTTAAATTGGTGAATCAACA+TGG 0.522743 6.1:+9586404 MS.gene83861:CDS
AAGGGATTGTTCTGAGGAGG+TGG 0.523100 6.1:-9585900 None:intergenic
GGAACGAGAATTGACCTTTG+TGG 0.525598 6.1:-9585879 None:intergenic
ACCAGATGTTTCCATCGAGA+TGG 0.544531 6.1:+9586080 MS.gene83861:CDS
TCGAAAGATTGAGAAATGAC+AGG 0.547098 6.1:-9586056 None:intergenic
TGAATCACACGCTCCAAACA+TGG 0.559827 6.1:-9585852 None:intergenic
AACAAGGGATTGTTCTGAGG+AGG 0.564533 6.1:-9585903 None:intergenic
TTGAGATGGTAGTTTAACAA+GGG 0.576755 6.1:-9585918 None:intergenic
TTTAACAAGGGATTGTTCTG+AGG 0.590649 6.1:-9585906 None:intergenic
CATGTAAATTAGTGTTGAGA+TGG 0.594522 6.1:-9585932 None:intergenic
TGTTAAGAAAACCATCTCGA+TGG 0.597227 6.1:-9586091 None:intergenic
GTTGAGATGGTAGTTTAACA+AGG 0.598487 6.1:-9585919 None:intergenic
AAAGAAATGGACAACCAATG+AGG 0.657128 6.1:+9586154 MS.gene83861:CDS
TTAAATTGGTGAATCAACAT+GGG 0.666593 6.1:+9586405 MS.gene83861:CDS
ATTGCAAGATTGATGAAGCG+AGG 0.667312 6.1:+9586446 MS.gene83861:CDS
AACGAGAATTGACCTTTGTG+GGG 0.672668 6.1:-9585877 None:intergenic
ATGCATGTCATCCATTTACG+TGG 0.700922 6.1:+9586014 MS.gene83861:CDS
GTGTGATTCATACCCCACAA+AGG 0.701235 6.1:+9585865 MS.gene83861:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! GTTTTTTTTAATGTTAAAAT+GGG + chr6.1:9586339-9586358 MS.gene83861:intron 10.0%
!!! TTTTTTTTAATGTTAAAATG+GGG + chr6.1:9586340-9586359 MS.gene83861:intron 10.0%
!!! GGTTTTTTTTAATGTTAAAA+TGG + chr6.1:9586338-9586357 MS.gene83861:intron 15.0%
!!! TTAATTTGTGATTTCATATA+GGG + chr6.1:9586376-9586395 MS.gene83861:intron 15.0%
!! AACCTTATATTGATGAAAAA+TGG - chr6.1:9586322-9586341 None:intergenic 20.0%
!! TTTAGAAAAAATCCAAAGAA+AGG - chr6.1:9586232-9586251 None:intergenic 20.0%
!!! CTTAATTTGTGATTTCATAT+AGG + chr6.1:9586375-9586394 MS.gene83861:intron 20.0%
!!! TACCATTTTTCATCAATATA+AGG + chr6.1:9586317-9586336 MS.gene83861:intron 20.0%
!!! TTTAAGATATTGGGATTATT+AGG - chr6.1:9585975-9585994 None:intergenic 20.0%
! TTAAATTGGTGAATCAACAT+GGG + chr6.1:9586405-9586424 MS.gene83861:CDS 25.0%
!! AGATGACTGTTTAAGATATT+GGG - chr6.1:9585984-9586003 None:intergenic 25.0%
!! ATTCTGGAAAAAGATTCAAA+AGG - chr6.1:9585830-9585849 None:intergenic 25.0%
!! TAGATGACTGTTTAAGATAT+TGG - chr6.1:9585985-9586004 None:intergenic 25.0%
!! TATATCTGTTTTCCTTTCTT+TGG + chr6.1:9586217-9586236 MS.gene83861:intron 25.0%
!! TTTTACATACATATCCTCAT+TGG - chr6.1:9586171-9586190 None:intergenic 25.0%
!!! ATATAGGGAACTTGTTAAAT+TGG + chr6.1:9586391-9586410 MS.gene83861:intron 25.0%
CATAAACCTTAATGTTTGGA+CGG - chr6.1:9586514-9586533 None:intergenic 30.0%
CTTATGCAATCAGAAAGAAA+TGG + chr6.1:9586141-9586160 MS.gene83861:CDS 30.0%
GGAACATAAACCTTAATGTT+TGG - chr6.1:9586518-9586537 None:intergenic 30.0%
GTTAAATTGGTGAATCAACA+TGG + chr6.1:9586404-9586423 MS.gene83861:CDS 30.0%
TATTAGGTACACTCAAGATA+TGG - chr6.1:9585959-9585978 None:intergenic 30.0%
TTCATCAATCTTGCAATTTG+AGG - chr6.1:9586443-9586462 None:intergenic 30.0%
TTGAGATGGTAGTTTAACAA+GGG - chr6.1:9585921-9585940 None:intergenic 30.0%
! CATGTAAATTAGTGTTGAGA+TGG - chr6.1:9585935-9585954 None:intergenic 30.0%
! TTTTCCAGAATATCCATGTT+TGG + chr6.1:9585839-9585858 MS.gene83861:CDS 30.0%
AAAGAAATGGACAACCAATG+AGG + chr6.1:9586154-9586173 MS.gene83861:CDS 35.0%
AAATGGATGACATGCATGTT+TGG - chr6.1:9586011-9586030 None:intergenic 35.0%
GTTGAGATGGTAGTTTAACA+AGG - chr6.1:9585922-9585941 None:intergenic 35.0%
TCGAAAGATTGAGAAATGAC+AGG - chr6.1:9586059-9586078 None:intergenic 35.0%
TGTTAAGAAAACCATCTCGA+TGG - chr6.1:9586094-9586113 None:intergenic 35.0%
TTTAACAAGGGATTGTTCTG+AGG - chr6.1:9585909-9585928 None:intergenic 35.0%
! ATCAACATGGGCTGAAAAAA+TGG + chr6.1:9586417-9586436 MS.gene83861:CDS 35.0%
AAACCGCGCTGTTCAATTAT+TGG + chr6.1:9586282-9586301 MS.gene83861:intron 40.0%
AACGAGAATTGACCTTTGTG+GGG - chr6.1:9585880-9585899 None:intergenic 40.0%
ATGATGACATGCCACGTAAA+TGG - chr6.1:9586028-9586047 None:intergenic 40.0%
ATGCATGTCATCCATTTACG+TGG + chr6.1:9586014-9586033 MS.gene83861:CDS 40.0%
ATTGCAAGATTGATGAAGCG+AGG + chr6.1:9586446-9586465 MS.gene83861:CDS 40.0%
CAAAACAGTGTCGTGATAGA+TGG + chr6.1:9586477-9586496 MS.gene83861:CDS 40.0%
CTACCAATAATTGAACAGCG+CGG - chr6.1:9586288-9586307 None:intergenic 40.0%
GAACGAGAATTGACCTTTGT+GGG - chr6.1:9585881-9585900 None:intergenic 40.0%
TCATCTCCGTCCAAACATTA+AGG + chr6.1:9586505-9586524 MS.gene83861:CDS 40.0%
TTGTTGACGTCTGGTACAAA+TGG - chr6.1:9586119-9586138 None:intergenic 40.0%
ACCAGATGTTTCCATCGAGA+TGG + chr6.1:9586080-9586099 MS.gene83861:CDS 45.0%
ACCATCTCGATGGAAACATC+TGG - chr6.1:9586084-9586103 None:intergenic 45.0%
CGCTCCAAACATGGATATTC+TGG - chr6.1:9585846-9585865 None:intergenic 45.0%
GGAACGAGAATTGACCTTTG+TGG - chr6.1:9585882-9585901 None:intergenic 45.0%
GTGTGATTCATACCCCACAA+AGG + chr6.1:9585865-9585884 MS.gene83861:CDS 45.0%
TGAATCACACGCTCCAAACA+TGG - chr6.1:9585855-9585874 None:intergenic 45.0%
!! AACAAGGGATTGTTCTGAGG+AGG - chr6.1:9585906-9585925 None:intergenic 45.0%
!! GCATAAGCTTTGTTGACGTC+TGG - chr6.1:9586128-9586147 None:intergenic 45.0%
!! AAGGGATTGTTCTGAGGAGG+TGG - chr6.1:9585903-9585922 None:intergenic 50.0%


Chromosome Type Strat End Strand Name
chr6.1 gene 9585789 9586541 9585789 ID=MS.gene83861
chr6.1 mRNA 9585789 9586541 9585789 ID=MS.gene83861.t1;Parent=MS.gene83861
chr6.1 exon 9585789 9586180 9585789 ID=MS.gene83861.t1.exon1;Parent=MS.gene83861.t1
chr6.1 CDS 9585789 9586180 9585789 ID=cds.MS.gene83861.t1;Parent=MS.gene83861.t1
chr6.1 exon 9586397 9586541 9586397 ID=MS.gene83861.t1.exon2;Parent=MS.gene83861.t1
chr6.1 CDS 9586397 9586541 9586397 ID=cds.MS.gene83861.t1;Parent=MS.gene83861.t1
Gene Sequence

>MS.gene83861

ATGGAACTCAATCTTAACAATCGAGCAAAGCATTCAAACCTTTTGAATCTTTTTCCAGAATATCCATGTTTGGAGCGTGTGATTCATACCCCACAAAGGTCAATTCTCGTTCCACCTCCTCAGAACAATCCCTTGTTAAACTACCATCTCAACACTAATTTACATGACCATATCTTGAGTGTACCTAATAATCCCAATATCTTAAACAGTCATCTATCTCCAAACATGCATGTCATCCATTTACGTGGCATGTCATCATCATTATCGCCTGTCATTTCTCAATCTTTCGAAACCAGATGTTTCCATCGAGATGGTTTTCTTAACACTCCATTTGTACCAGACGTCAACAAAGCTTATGCAATCAGAAAGAAATGGACAACCAATGAGGATATGTATGTAAAATATTTATTCATTTATTAATCTCTCTCTATATCTGTTTTCCTTTCTTTGGATTTTTTCTAAAAAAAATATATATAATAGAATTAAATTACATAAACCGCGCTGTTCAATTATTGGTAGTTTTATAGATACCATTTTTCATCAATATAAGGTTTTTTTTAATGTTAAAATGGGGTGAGTGTTTAATCTTAATTTGTGATTTCATATAGGGAACTTGTTAAATTGGTGAATCAACATGGGCTGAAAAAATGGCCTCAAATTGCAAGATTGATGAAGCGAGGAAGAAATGCAAAACAGTGTCGTGATAGATGGCTCAATCATCTCCGTCCAAACATTAAGGTTTATGTTCCCTAA
Protein sequence

>MS.gene83861.t1

MELNLNNRAKHSNLLNLFPEYPCLERVIHTPQRSILVPPPQNNPLLNYHLNTNLHDHILSVPNNPNILNSHLSPNMHVIHLRGMSSSLSPVISQSFETRCFHRDGFLNTPFVPDVNKAYAIRKKWTTNEDMELVKLVNQHGLKKWPQIARLMKRGRNAKQCRDRWLNHLRPNIKVYVP