AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene83868

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene83868.t1 MTR_4g088015 66.667 54 17 1 121 174 220 272 2.98e-17 78.6
MS.gene83868.t1 MTR_3g463400 57.407 54 22 1 121 174 132 184 4.76e-15 72.4
MS.gene83868.t1 MTR_5g070020 57.407 54 22 1 121 174 121 173 1.16e-14 70.9
MS.gene83868.t1 MTR_5g049190 52.542 59 27 1 116 174 13 70 1.41e-14 69.7
MS.gene83868.t1 MTR_7g451170 57.407 54 22 1 121 174 190 242 2.47e-14 70.1
MS.gene83868.t1 MTR_7g037260 55.556 54 23 1 121 174 144 196 2.40e-13 67.0
MS.gene83868.t1 MTR_7g035350 52.727 55 25 1 120 174 223 276 2.67e-13 67.4
MS.gene83868.t1 MTR_3g077650 55.556 54 23 1 121 174 180 232 4.38e-13 66.6
MS.gene83868.t1 MTR_1g057980 56.364 55 22 2 121 174 78 131 8.46e-13 65.5
MS.gene83868.t1 MTR_4g105660 44.156 77 35 2 108 177 159 234 2.69e-12 64.3
MS.gene83868.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.gene83868.t1 AT3G27785 58.621 58 23 1 117 174 184 240 1.28e-15 73.9
MS.gene83868.t1 AT5G58850 53.704 54 24 1 121 174 104 156 3.56e-14 69.7
MS.gene83868.t1 AT5G11050 55.556 54 23 1 121 174 104 156 3.84e-14 69.7
MS.gene83868.t1 AT4G18770 47.541 61 31 1 114 174 209 268 1.25e-13 68.2
MS.gene83868.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:-9565621 MS.gene83868:intron
TAGATGACTGTTTAAGATAT+TGG 0.217151 6.1:+9566030 None:intergenic
CGCTCCAAACATGGATATTC+TGG 0.220757 6.1:+9566169 None:intergenic
TTTAAGATATTGGGATTATT+AGG 0.225450 6.1:+9566040 None:intergenic
TCATCTCCGTCCAAACATTA+AGG 0.270772 6.1:-9565507 MS.gene83868:CDS
AGATGACTGTTTAAGATATT+GGG 0.311205 6.1:+9566031 None:intergenic
ATGATGACATGCCACGTAAA+TGG 0.337422 6.1:+9565987 None:intergenic
GGAACATAAACCTTAATGTT+TGG 0.342814 6.1:+9565497 None:intergenic
TTCATCAATCTTGCAATTTG+AGG 0.352946 6.1:+9565572 None:intergenic
GCATAAGCTTTGTTGACGTC+TGG 0.422118 6.1:+9565887 None:intergenic
CAAAACAGTGTCGTGATAGA+TGG 0.437524 6.1:-9565535 MS.gene83868:CDS
GAACGAGAATTGACCTTTGT+GGG 0.444047 6.1:+9566134 None:intergenic
AAATGGATGACATGCATGTT+TGG 0.446835 6.1:+9566004 None:intergenic
TTGTTGACGTCTGGTACAAA+TGG 0.468340 6.1:+9565896 None:intergenic
TATTAGGTACACTCAAGATA+TGG 0.470686 6.1:+9566056 None:intergenic
ACCATCTCGATGGAAACATC+TGG 0.493183 6.1:+9565931 None:intergenic
CTTATGCAATCAGAAAGAAA+TGG 0.496059 6.1:-9565871 MS.gene83868:CDS
CATAAACCTTAATGTTTGGA+CGG 0.508200 6.1:+9565501 None:intergenic
GTTAAATTGGTGAATCAACA+TGG 0.522743 6.1:-9565608 MS.gene83868:CDS
AAGGGATTGTTCTGAGGAGG+TGG 0.523100 6.1:+9566112 None:intergenic
GGAACGAGAATTGACCTTTG+TGG 0.525598 6.1:+9566133 None:intergenic
ACCAGATGTTTCCATCGAGA+TGG 0.544531 6.1:-9565932 MS.gene83868:CDS
TCGAAAGATTGAGAAATGAC+AGG 0.547098 6.1:+9565956 None:intergenic
TGAATCACACGCTCCAAACA+TGG 0.559827 6.1:+9566160 None:intergenic
AACAAGGGATTGTTCTGAGG+AGG 0.564533 6.1:+9566109 None:intergenic
TTGAGATGGTAGTTTAACAA+GGG 0.576755 6.1:+9566094 None:intergenic
TTTAACAAGGGATTGTTCTG+AGG 0.590649 6.1:+9566106 None:intergenic
CATGTAAATTAGTGTTGAGA+TGG 0.594522 6.1:+9566080 None:intergenic
TGTTAAGAAAACCATCTCGA+TGG 0.597227 6.1:+9565921 None:intergenic
GTTGAGATGGTAGTTTAACA+AGG 0.598487 6.1:+9566093 None:intergenic
AAAGAAATGGACAACCAATG+AGG 0.657128 6.1:-9565858 MS.gene83868:CDS
TTAAATTGGTGAATCAACAT+GGG 0.666593 6.1:-9565607 MS.gene83868:CDS
ATTGCAAGATTGATGAAGCG+AGG 0.667312 6.1:-9565566 MS.gene83868:CDS
AACGAGAATTGACCTTTGTG+GGG 0.672668 6.1:+9566135 None:intergenic
ATGCATGTCATCCATTTACG+TGG 0.700922 6.1:-9565998 MS.gene83868:CDS
GTGTGATTCATACCCCACAA+AGG 0.701235 6.1:-9566147 MS.gene83868:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! GTTTTTTTTAATGTTAAAAT+GGG - chr6.1:9566043-9566062 MS.gene83868:CDS 10.0%
!!! TTTTTTTTAATGTTAAAATG+GGG - chr6.1:9566044-9566063 MS.gene83868:CDS 10.0%
!!! GGTTTTTTTTAATGTTAAAA+TGG - chr6.1:9566042-9566061 MS.gene83868:CDS 15.0%
!!! TTAATTTGTGATTTCATATA+GGG - chr6.1:9566080-9566099 MS.gene83868:CDS 15.0%
!! AACCTTATATTGATGAAAAA+TGG + chr6.1:9566026-9566045 None:intergenic 20.0%
!! TTTAGAAAAAATCCAAAGAA+AGG + chr6.1:9565936-9565955 None:intergenic 20.0%
!!! CTTAATTTGTGATTTCATAT+AGG - chr6.1:9566079-9566098 MS.gene83868:CDS 20.0%
!!! TACCATTTTTCATCAATATA+AGG - chr6.1:9566021-9566040 MS.gene83868:CDS 20.0%
!!! TTTAAGATATTGGGATTATT+AGG + chr6.1:9565679-9565698 None:intergenic 20.0%
! TTAAATTGGTGAATCAACAT+GGG - chr6.1:9566109-9566128 MS.gene83868:CDS 25.0%
!! AGATGACTGTTTAAGATATT+GGG + chr6.1:9565688-9565707 None:intergenic 25.0%
!! ATTCTGGAAAAAGATTCAAA+AGG + chr6.1:9565534-9565553 None:intergenic 25.0%
!! TAGATGACTGTTTAAGATAT+TGG + chr6.1:9565689-9565708 None:intergenic 25.0%
!! TATATCTGTTTTCCTTTCTT+TGG - chr6.1:9565921-9565940 MS.gene83868:CDS 25.0%
!! TTTTACATACATATCCTCAT+TGG + chr6.1:9565875-9565894 None:intergenic 25.0%
!!! ATATAGGGAACTTGTTAAAT+TGG - chr6.1:9566095-9566114 MS.gene83868:CDS 25.0%
CATAAACCTTAATGTTTGGA+CGG + chr6.1:9566218-9566237 None:intergenic 30.0%
CTTATGCAATCAGAAAGAAA+TGG - chr6.1:9565845-9565864 MS.gene83868:intron 30.0%
GGAACATAAACCTTAATGTT+TGG + chr6.1:9566222-9566241 None:intergenic 30.0%
GTTAAATTGGTGAATCAACA+TGG - chr6.1:9566108-9566127 MS.gene83868:CDS 30.0%
TATTAGGTACACTCAAGATA+TGG + chr6.1:9565663-9565682 None:intergenic 30.0%
TTCATCAATCTTGCAATTTG+AGG + chr6.1:9566147-9566166 None:intergenic 30.0%
TTGAGATGGTAGTTTAACAA+GGG + chr6.1:9565625-9565644 None:intergenic 30.0%
! CATGTAAATTAGTGTTGAGA+TGG + chr6.1:9565639-9565658 None:intergenic 30.0%
! TTTTCCAGAATATCCATGTT+TGG - chr6.1:9565543-9565562 MS.gene83868:CDS 30.0%
AAAGAAATGGACAACCAATG+AGG - chr6.1:9565858-9565877 MS.gene83868:CDS 35.0%
AAATGGATGACATGCATGTT+TGG + chr6.1:9565715-9565734 None:intergenic 35.0%
GTTGAGATGGTAGTTTAACA+AGG + chr6.1:9565626-9565645 None:intergenic 35.0%
TCGAAAGATTGAGAAATGAC+AGG + chr6.1:9565763-9565782 None:intergenic 35.0%
TGTTAAGAAAACCATCTCGA+TGG + chr6.1:9565798-9565817 None:intergenic 35.0%
TTTAACAAGGGATTGTTCTG+AGG + chr6.1:9565613-9565632 None:intergenic 35.0%
! ATCAACATGGGCTGAAAAAA+TGG - chr6.1:9566121-9566140 MS.gene83868:CDS 35.0%
AAACCGCGCTGTTCAATTAT+TGG - chr6.1:9565986-9566005 MS.gene83868:CDS 40.0%
AACGAGAATTGACCTTTGTG+GGG + chr6.1:9565584-9565603 None:intergenic 40.0%
ATGATGACATGCCACGTAAA+TGG + chr6.1:9565732-9565751 None:intergenic 40.0%
ATGCATGTCATCCATTTACG+TGG - chr6.1:9565718-9565737 MS.gene83868:intron 40.0%
ATTGCAAGATTGATGAAGCG+AGG - chr6.1:9566150-9566169 MS.gene83868:CDS 40.0%
CAAAACAGTGTCGTGATAGA+TGG - chr6.1:9566181-9566200 MS.gene83868:CDS 40.0%
CTACCAATAATTGAACAGCG+CGG + chr6.1:9565992-9566011 None:intergenic 40.0%
GAACGAGAATTGACCTTTGT+GGG + chr6.1:9565585-9565604 None:intergenic 40.0%
TCATCTCCGTCCAAACATTA+AGG - chr6.1:9566209-9566228 MS.gene83868:CDS 40.0%
TTGTTGACGTCTGGTACAAA+TGG + chr6.1:9565823-9565842 None:intergenic 40.0%
ACCAGATGTTTCCATCGAGA+TGG - chr6.1:9565784-9565803 MS.gene83868:intron 45.0%
ACCATCTCGATGGAAACATC+TGG + chr6.1:9565788-9565807 None:intergenic 45.0%
CGCTCCAAACATGGATATTC+TGG + chr6.1:9565550-9565569 None:intergenic 45.0%
GGAACGAGAATTGACCTTTG+TGG + chr6.1:9565586-9565605 None:intergenic 45.0%
GTGTGATTCATACCCCACAA+AGG - chr6.1:9565569-9565588 MS.gene83868:CDS 45.0%
TGAATCACACGCTCCAAACA+TGG + chr6.1:9565559-9565578 None:intergenic 45.0%
!! AACAAGGGATTGTTCTGAGG+AGG + chr6.1:9565610-9565629 None:intergenic 45.0%
!! GCATAAGCTTTGTTGACGTC+TGG + chr6.1:9565832-9565851 None:intergenic 45.0%
!! AAGGGATTGTTCTGAGGAGG+TGG + chr6.1:9565607-9565626 None:intergenic 50.0%


Chromosome Type Strat End Strand Name
chr6.1 gene 9565493 9566245 9565493 ID=MS.gene83868
chr6.1 mRNA 9565493 9566245 9565493 ID=MS.gene83868.t1;Parent=MS.gene83868
chr6.1 exon 9565854 9566245 9565854 ID=MS.gene83868.t1.exon1;Parent=MS.gene83868.t1
chr6.1 CDS 9565854 9566245 9565854 ID=cds.MS.gene83868.t1;Parent=MS.gene83868.t1
chr6.1 exon 9565493 9565637 9565493 ID=MS.gene83868.t1.exon2;Parent=MS.gene83868.t1
chr6.1 CDS 9565493 9565637 9565493 ID=cds.MS.gene83868.t1;Parent=MS.gene83868.t1
Gene Sequence

>MS.gene83868

ATGGAACTCAATCTTAACAATCGAGCAAAGCATTCAAACCTTTTGAATCTTTTTCCAGAATATCCATGTTTGGAGCGTGTGATTCATACCCCACAAAGGTCAATTCTCGTTCCACCTCCTCAGAACAATCCCTTGTTAAACTACCATCTCAACACTAATTTACATGACCATATCTTGAGTGTACCTAATAATCCCAATATCTTAAACAGTCATCTATCTCCAAACATGCATGTCATCCATTTACGTGGCATGTCATCATCATTATCGCCTGTCATTTCTCAATCTTTCGAAACCAGATGTTTCCATCGAGATGGTTTTCTTAACACTCCATTTGTACCAGACGTCAACAAAGCTTATGCAATCAGAAAGAAATGGACAACCAATGAGGATATGTATGTAAAATATTTATTCATTTATTAATCTCTCTCTATATCTGTTTTCCTTTCTTTGGATTTTTTCTAAAAAAAATATATATAATAGAATTAAATTACATAAACCGCGCTGTTCAATTATTGGTAGTTTTATAGATACCATTTTTCATCAATATAAGGTTTTTTTTAATGTTAAAATGGGGTGAGTGTTTAATCTTAATTTGTGATTTCATATAGGGAACTTGTTAAATTGGTGAATCAACATGGGCTGAAAAAATGGCCTCAAATTGCAAGATTGATGAAGCGAGGAAGAAATGCAAAACAGTGTCGTGATAGATGGCTCAATCATCTCCGTCCAAACATTAAGGTTTATGTTCCCTAA
Protein sequence

>MS.gene83868.t1

MELNLNNRAKHSNLLNLFPEYPCLERVIHTPQRSILVPPPQNNPLLNYHLNTNLHDHILSVPNNPNILNSHLSPNMHVIHLRGMSSSLSPVISQSFETRCFHRDGFLNTPFVPDVNKAYAIRKKWTTNEDMELVKLVNQHGLKKWPQIARLMKRGRNAKQCRDRWLNHLRPNIKVYVP