AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene039591

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene039591.t1 MTR_3g013635 99.301 143 1 0 1 143 1 143 1.93e-105 297
MS.gene039591.t1 MTR_3g013635 99.301 143 1 0 1 143 1 143 1.93e-105 297
MS.gene039591.t1 MTR_8g040740 88.811 143 16 0 1 143 1 143 1.63e-97 277
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene039591.t1 AT5G61170 83.099 142 24 0 1 142 1 142 1.30e-90 259
MS.gene039591.t1 AT3G02080 81.119 143 27 0 1 143 1 143 1.36e-90 259
MS.gene039591.t1 AT5G15520 83.453 139 23 0 1 139 1 139 9.16e-89 254

Find 47 sgRNAs with CRISPR-Local

Find 93 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TGTGAAGACTGCAAGGTTTA+AGG 0.181111 3.1:+9076844 MS.gene039591:CDS
GGTGCATTCCAGAGGATTTA+TGG 0.279212 3.1:+9077082 MS.gene039591:CDS
TTCCAGTGGCAGGAGGGATT+TGG 0.312675 3.1:+9077517 MS.gene039591:CDS
TTCACAATATCTGTCCATTC+TGG 0.341460 3.1:-9076827 None:intergenic
AGGGATTTGGACCAAGTTGC+TGG 0.349640 3.1:+9077530 MS.gene039591:CDS
CCTTGGTGTCCATCTCAATA+AGG 0.385015 3.1:-9077198 None:intergenic
GACTGCAAGGTTTAAGGAGT+TGG 0.416477 3.1:+9076850 MS.gene039591:CDS
ACCCCTCAAGTAGATCTTCC+TGG 0.431786 3.1:-9077047 None:intergenic
GTCCAAATCCCTCCTGCCAC+TGG 0.442468 3.1:-9077519 None:intergenic
GACTTCCACCATAAATCCTC+TGG 0.453242 3.1:-9077090 None:intergenic
ATCTACTTGAGGGGTGGACT+CGG 0.454423 3.1:+9077055 MS.gene039591:CDS
TCTGCTCATCTCAAAAGATC+TGG 0.481965 3.1:+9075910 MS.gene039591:CDS
GTGCCGCAGCTTCCATGGCC+AGG 0.485644 3.1:+9077029 MS.gene039591:intron
GCTCTGACGTAGTACCAGTC+AGG 0.489319 3.1:-9076884 None:intergenic
TAGTACCAGTCAGGGTCATA+AGG 0.498306 3.1:-9076875 None:intergenic
TATGGTGGAAGTCAGAGAAA+TGG 0.514768 3.1:+9077100 MS.gene039591:CDS
CAAGTAGATCTTCCTGGCCA+TGG 0.517027 3.1:-9077041 None:intergenic
GGCCAGGAAGATCTACTTGA+GGG 0.518439 3.1:+9077045 MS.gene039591:CDS
TTGAGGGGTGGACTCGGTGT+TGG 0.522669 3.1:+9077061 MS.gene039591:CDS
GGAAGATCACTTCCAGTGGC+AGG 0.522712 3.1:+9077507 MS.gene039591:CDS
AACAGTCCTTGCGGTAGCCA+TGG 0.523894 3.1:-9075851 None:intergenic
TAACAATACGTCCAGCAACT+TGG 0.533492 3.1:-9077541 None:intergenic
TGGCTCCTTATGACCCTGAC+TGG 0.535373 3.1:+9076870 MS.gene039591:CDS
CCACTGCTCTTGCAGAAATG+AGG 0.542089 3.1:-9077133 None:intergenic
GACTGGTACTACGTCAGAGC+TGG 0.543992 3.1:+9076887 MS.gene039591:CDS
AACAGATGGAGCTTCCAGAA+TGG 0.551656 3.1:+9076813 MS.gene039591:intron
TTGAAGAATGTGGCGAGCAA+TGG 0.555153 3.1:-9077158 None:intergenic
GAACATGAACCTTATTGAGA+TGG 0.561257 3.1:+9077189 MS.gene039591:CDS
CCTCATTTCTGCAAGAGCAG+TGG 0.589477 3.1:+9077133 MS.gene039591:CDS
TCGGTGTTGGTGCATTCCAG+AGG 0.603387 3.1:+9077074 MS.gene039591:CDS
AGATCACTTCCAGTGGCAGG+AGG 0.615298 3.1:+9077510 MS.gene039591:CDS
CAGATATTGTGAAGACTGCA+AGG 0.617924 3.1:+9076837 MS.gene039591:CDS
CTGCTCTTGCAGAAATGAGG+TGG 0.621206 3.1:-9077130 None:intergenic
AGGAAGATCTACTTGAGGGG+TGG 0.621735 3.1:+9077049 MS.gene039591:CDS
CTCTGACGTAGTACCAGTCA+GGG 0.627550 3.1:-9076883 None:intergenic
TCATCTCAAAAGATCTGGCA+AGG 0.635281 3.1:+9075915 MS.gene039591:CDS
GCACAACCATGGCTACCGCA+AGG 0.635383 3.1:+9075845 None:intergenic
GATCACTTCCAGTGGCAGGA+GGG 0.646734 3.1:+9077511 MS.gene039591:CDS
CTTATTGAGATGGACACCAA+GGG 0.649426 3.1:+9077199 MS.gene039591:CDS
TGGCCAGGAAGATCTACTTG+AGG 0.650322 3.1:+9077044 MS.gene039591:CDS
GGCAGGAAGATCACTTCCAG+TGG 0.650796 3.1:+9077503 MS.gene039591:CDS
CCTTATTGAGATGGACACCA+AGG 0.671459 3.1:+9077198 MS.gene039591:CDS
GCATTCCAGAGGATTTATGG+TGG 0.673361 3.1:+9077085 MS.gene039591:CDS
AACATCTTGAACAGTCCTTG+CGG 0.675305 3.1:-9075860 None:intergenic
TCTGCAACTGTTGAAGAATG+TGG 0.679137 3.1:-9077168 None:intergenic
GCCAGGAAGATCTACTTGAG+GGG 0.686642 3.1:+9077046 MS.gene039591:CDS
TTATTGAGATGGACACCAAG+GGG 0.704884 3.1:+9077200 MS.gene039591:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTTTTTGTTAATTTAAACAA+GGG - chr3.1:9076949-9076968 None:intergenic 10.0%
!!! TTTTTTTGTTAATTTAAACA+AGG - chr3.1:9076950-9076969 None:intergenic 10.0%
!! TAATCTATGTAATTAGAATA+AGG - chr3.1:9076581-9076600 None:intergenic 15.0%
!!! AAAACCAAAATGAAATTTTT+CGG - chr3.1:9075953-9075972 None:intergenic 15.0%
!!! ATCAAAAACATTTTTTTGTT+AGG - chr3.1:9076256-9076275 None:intergenic 15.0%
!!! TTAATGTTATGTTTTATGTT+AGG + chr3.1:9076160-9076179 MS.gene039591:intron 15.0%
!!! TTGTTTTTGTTAATCAAATT+AGG + chr3.1:9076457-9076476 MS.gene039591:intron 15.0%
!!! TTTTGATTTTTTTTTTGAAG+AGG + chr3.1:9076001-9076020 MS.gene039591:intron 15.0%
!! AACAAAAAAATAACTTTCGA+GGG + chr3.1:9076960-9076979 MS.gene039591:intron 20.0%
!! ATGTTAAAAACATGATATGA+AGG - chr3.1:9077463-9077482 None:intergenic 20.0%
!! TAACAAAAAAATAACTTTCG+AGG + chr3.1:9076959-9076978 MS.gene039591:intron 20.0%
!! TCTAATTACATAGATTACTT+GGG + chr3.1:9076584-9076603 MS.gene039591:intron 20.0%
!! TGTTAAAAACATGATATGAA+GGG - chr3.1:9077462-9077481 None:intergenic 20.0%
!! TTATAATGATACGAATGAAA+TGG + chr3.1:9076714-9076733 MS.gene039591:intron 20.0%
!! TTCTAATTACATAGATTACT+TGG + chr3.1:9076583-9076602 MS.gene039591:intron 20.0%
!! TTGTATAGTTCAAATTTAGT+TGG + chr3.1:9076745-9076764 MS.gene039591:intron 20.0%
!!! ACAAATTTTGAAAGTTCAAA+AGG - chr3.1:9076550-9076569 None:intergenic 20.0%
!!! ATTTGTTTTGATTTGCTTAA+CGG + chr3.1:9076025-9076044 MS.gene039591:intron 20.0%
!!! CAAATTTTGAAAGTTCAAAA+GGG - chr3.1:9076549-9076568 None:intergenic 20.0%
!!! TAACTATTTGATTTACATTG+CGG - chr3.1:9077313-9077332 None:intergenic 20.0%
!!! TGTTTTTGATTTGATTTGAT+TGG + chr3.1:9076266-9076285 MS.gene039591:intron 20.0%
!!! TTGTCAAATTAATCTGTTTT+AGG + chr3.1:9076060-9076079 MS.gene039591:intron 20.0%
!! GTTATGTTTTATGTTAGGTT+TGG + chr3.1:9076165-9076184 MS.gene039591:intron 25.0%
!! TTCACCGAAAAATTTCATTT+TGG + chr3.1:9075946-9075965 MS.gene039591:intron 25.0%
!! TTGATTTTTCTTTATCACAG+TGG + chr3.1:9077482-9077501 MS.gene039591:intron 25.0%
!!! GAACTTTCAAAATTTGTTGT+TGG + chr3.1:9076553-9076572 MS.gene039591:intron 25.0%
!!! GTGCTTTTATTTATAGTGAT+TGG + chr3.1:9077399-9077418 MS.gene039591:intron 25.0%
!!! TTTGTTTTGATTTGCTTAAC+GGG + chr3.1:9076026-9076045 MS.gene039591:intron 25.0%
CATCTGTTCATAACAAAACA+AGG - chr3.1:9076801-9076820 None:intergenic 30.0%
! ACATTGCAATTTTCAACAAC+AGG - chr3.1:9077002-9077021 None:intergenic 30.0%
!!! CTTGTTTTGTTATGAACAGA+TGG + chr3.1:9076799-9076818 MS.gene039591:intron 30.0%
AACTACTGCTCAACAAATGT+TGG - chr3.1:9077362-9077381 None:intergenic 35.0%
GAACATGAACCTTATTGAGA+TGG + chr3.1:9077189-9077208 MS.gene039591:CDS 35.0%
GTTAATTTAAACAAGGGACC+AGG - chr3.1:9076943-9076962 None:intergenic 35.0%
TACGGTTTACAATAGGGAAT+AGG + chr3.1:9077251-9077270 MS.gene039591:intron 35.0%
TCAGAAAACTAGTGACATGA+TGG + chr3.1:9076368-9076387 MS.gene039591:intron 35.0%
TTACATAGATTACTTGGGCA+TGG + chr3.1:9076589-9076608 MS.gene039591:intron 35.0%
TTCACAATATCTGTCCATTC+TGG - chr3.1:9076830-9076849 None:intergenic 35.0%
! TTATCTTTGTTAGCCTGCTA+CGG + chr3.1:9077233-9077252 MS.gene039591:intron 35.0%
! TTTTTCTTTATCACAGTGGC+AGG + chr3.1:9077486-9077505 MS.gene039591:intron 35.0%
!! GTTTGATTTTGTGCATTTCC+TGG + chr3.1:9076922-9076941 MS.gene039591:intron 35.0%
AACATCTTGAACAGTCCTTG+CGG - chr3.1:9075863-9075882 None:intergenic 40.0%
CAGATATTGTGAAGACTGCA+AGG + chr3.1:9076837-9076856 MS.gene039591:CDS 40.0%
CTTATTGAGATGGACACCAA+GGG + chr3.1:9077199-9077218 MS.gene039591:CDS 40.0%
GATAATGAGTTCTTACCCCT+TGG - chr3.1:9077218-9077237 None:intergenic 40.0%
GCTCAACAAATGTTGGTATC+AGG - chr3.1:9077355-9077374 None:intergenic 40.0%
GTATTCAAGCTCTACTTCAC+TGG + chr3.1:9076680-9076699 MS.gene039591:intron 40.0%
TAACAATACGTCCAGCAACT+TGG - chr3.1:9077544-9077563 None:intergenic 40.0%
TCATCTCAAAAGATCTGGCA+AGG + chr3.1:9075915-9075934 MS.gene039591:CDS 40.0%
TCTGCAACTGTTGAAGAATG+TGG - chr3.1:9077171-9077190 None:intergenic 40.0%
TCTGCTCATCTCAAAAGATC+TGG + chr3.1:9075910-9075929 MS.gene039591:CDS 40.0%
TGTGAAGACTGCAAGGTTTA+AGG + chr3.1:9076844-9076863 MS.gene039591:CDS 40.0%
TTATTGAGATGGACACCAAG+GGG + chr3.1:9077200-9077219 MS.gene039591:CDS 40.0%
! TATGGTGGAAGTCAGAGAAA+TGG + chr3.1:9077100-9077119 MS.gene039591:CDS 40.0%
AACAGATGGAGCTTCCAGAA+TGG + chr3.1:9076813-9076832 MS.gene039591:intron 45.0%
AGCCTGCTACGGTTTACAAT+AGG + chr3.1:9077244-9077263 MS.gene039591:intron 45.0%
CATGGTTTCAACTCACGTGT+TGG + chr3.1:9076607-9076626 MS.gene039591:intron 45.0%
CCTTATTGAGATGGACACCA+AGG + chr3.1:9077198-9077217 MS.gene039591:CDS 45.0%
GACTGCAAGGTTTAAGGAGT+TGG + chr3.1:9076850-9076869 MS.gene039591:CDS 45.0%
GACTTCCACCATAAATCCTC+TGG - chr3.1:9077093-9077112 None:intergenic 45.0%
GCATTCCAGAGGATTTATGG+TGG + chr3.1:9077085-9077104 MS.gene039591:CDS 45.0%
GCCTGCTACGGTTTACAATA+GGG + chr3.1:9077245-9077264 MS.gene039591:intron 45.0%
GGTGCATTCCAGAGGATTTA+TGG + chr3.1:9077082-9077101 MS.gene039591:CDS 45.0%
TAGTACCAGTCAGGGTCATA+AGG - chr3.1:9076878-9076897 None:intergenic 45.0%
TCCCTATTGTAAACCGTAGC+AGG - chr3.1:9077249-9077268 None:intergenic 45.0%
TTGAAGAATGTGGCGAGCAA+TGG - chr3.1:9077161-9077180 None:intergenic 45.0%
!! CCTTGGTGTCCATCTCAATA+AGG - chr3.1:9077201-9077220 None:intergenic 45.0%
ACCCCTCAAGTAGATCTTCC+TGG - chr3.1:9077050-9077069 None:intergenic 50.0%
AGGAAGATCTACTTGAGGGG+TGG + chr3.1:9077049-9077068 MS.gene039591:CDS 50.0%
AGGGATTTGGACCAAGTTGC+TGG + chr3.1:9077530-9077549 MS.gene039591:CDS 50.0%
CAAGTAGATCTTCCTGGCCA+TGG - chr3.1:9077044-9077063 None:intergenic 50.0%
CCACTGCTCTTGCAGAAATG+AGG - chr3.1:9077136-9077155 None:intergenic 50.0%
CCTCATTTCTGCAAGAGCAG+TGG + chr3.1:9077133-9077152 MS.gene039591:CDS 50.0%
CTCTGACGTAGTACCAGTCA+GGG - chr3.1:9076886-9076905 None:intergenic 50.0%
CTGCTCTTGCAGAAATGAGG+TGG - chr3.1:9077133-9077152 None:intergenic 50.0%
GCCAGGAAGATCTACTTGAG+GGG + chr3.1:9077046-9077065 MS.gene039591:CDS 50.0%
GGCCAGGAAGATCTACTTGA+GGG + chr3.1:9077045-9077064 MS.gene039591:CDS 50.0%
TGGCCAGGAAGATCTACTTG+AGG + chr3.1:9077044-9077063 MS.gene039591:CDS 50.0%
! ATCTACTTGAGGGGTGGACT+CGG + chr3.1:9077055-9077074 MS.gene039591:CDS 50.0%
! TTTTTGTGCCGCAGCTTCCA+TGG + chr3.1:9077024-9077043 MS.gene039591:intron 50.0%
AGATCACTTCCAGTGGCAGG+AGG + chr3.1:9077510-9077529 MS.gene039591:CDS 55.0%
GACTGGTACTACGTCAGAGC+TGG + chr3.1:9076887-9076906 MS.gene039591:CDS 55.0%
GATCACTTCCAGTGGCAGGA+GGG + chr3.1:9077511-9077530 MS.gene039591:CDS 55.0%
GCTCTGACGTAGTACCAGTC+AGG - chr3.1:9076887-9076906 None:intergenic 55.0%
GGAAGATCACTTCCAGTGGC+AGG + chr3.1:9077507-9077526 MS.gene039591:CDS 55.0%
GGCAGGAAGATCACTTCCAG+TGG + chr3.1:9077503-9077522 MS.gene039591:CDS 55.0%
TGGCTCCTTATGACCCTGAC+TGG + chr3.1:9076870-9076889 MS.gene039591:CDS 55.0%
TTCCAGTGGCAGGAGGGATT+TGG + chr3.1:9077517-9077536 MS.gene039591:CDS 55.0%
!! TCGGTGTTGGTGCATTCCAG+AGG + chr3.1:9077074-9077093 MS.gene039591:CDS 55.0%
CTTCCTGGCCATGGAAGCTG+CGG - chr3.1:9077035-9077054 None:intergenic 60.0%
GTCCAAATCCCTCCTGCCAC+TGG - chr3.1:9077522-9077541 None:intergenic 60.0%
!! TTGAGGGGTGGACTCGGTGT+TGG + chr3.1:9077061-9077080 MS.gene039591:CDS 60.0%
GTGCCGCAGCTTCCATGGCC+AGG + chr3.1:9077029-9077048 MS.gene039591:intron 70.0%


Chromosome Type Strat End Strand Name
chr3.1 gene 9075853 9077574 9075853 ID=MS.gene039591
chr3.1 mRNA 9075853 9077574 9075853 ID=MS.gene039591.t1;Parent=MS.gene039591
chr3.1 exon 9075853 9075936 9075853 ID=MS.gene039591.t1.exon1;Parent=MS.gene039591.t1
chr3.1 CDS 9075853 9075936 9075853 ID=cds.MS.gene039591.t1;Parent=MS.gene039591.t1
chr3.1 exon 9076818 9076908 9076818 ID=MS.gene039591.t1.exon2;Parent=MS.gene039591.t1
chr3.1 CDS 9076818 9076908 9076818 ID=cds.MS.gene039591.t1;Parent=MS.gene039591.t1
chr3.1 exon 9077038 9077221 9077038 ID=MS.gene039591.t1.exon3;Parent=MS.gene039591.t1
chr3.1 CDS 9077038 9077221 9077038 ID=cds.MS.gene039591.t1;Parent=MS.gene039591.t1
chr3.1 exon 9077502 9077574 9077502 ID=MS.gene039591.t1.exon4;Parent=MS.gene039591.t1
chr3.1 CDS 9077502 9077574 9077502 ID=cds.MS.gene039591.t1;Parent=MS.gene039591.t1
Gene Sequence

>MS.gene039591

ATGGCTACCGCAAGGACTGTTCAAGATGTTTCTTCACACGAGTTTGTCAAAGCTTACTCTGCTCATCTCAAAAGATCTGGCAAGGTTAATCAATTCACCGAAAAATTTCATTTTGGTTTTCTATTTTGATTGTGTATGATTCGATTTGTTTTGATTTTTTTTTTGAAGAGGAATTTGTTTTGATTTGCTTAACGGGTTCATGAATTTTTGTCAAATTAATCTGTTTTAGGAGCTTTTGTGTTTTTGTTATTTTTTATTAGTTTATAAATTGTCATGCTTTATTGTTTAGATTTGTGTTTTTGTGTTTTTAATGTTATGTTTTATGTTAGGTTTGGTTAAAGTTTATAACTTGATCTACTTCGTTGCTGTGTCTTGTTGAATGTAGTTTTGTTTGTCTAATCCTAACAAAAAAATGTTTTTGATTTGATTTGATTGGATTAATAAATAGAAAAATGTTCGTTGTGATGTTAATATGCTGTAATTTTTACAAGTGATTGATTCAGAGTAAGCATTTGTCAGAAAACTAGTGACATGATGGATTTGTGATTTTTCTCTTACACTTGTTTTTGATTAGTTTTAGTGAAAACATTCAAGTTGATTATGATTGTTTTTGTTAATCAAATTAGGAATGATTTTCTGTATTATATGATGTTGATGACAGTTTTTATTTTTTTATGCTATGAATTGTAATGTCCCTTTTGAACTTTCAAAATTTGTTGTTGGATCCTTATTCTAATTACATAGATTACTTGGGCATGGTTTCAACTCACGTGTTGGCTTAGTTTTAGAAATAACTTTCATTATGCTTTTGATTTTTTATGTATTATGTATTCAAGCTCTACTTCACTGGTGTGATCTAGTTTATAATGATACGAATGAAATGGCTGTGTAATTGTATAGTTCAAATTTAGTTGGATTATTATTCTAATTATAGTTTTTTGTTTTCCTTGTTTTGTTATGAACAGATGGAGCTTCCAGAATGGACAGATATTGTGAAGACTGCAAGGTTTAAGGAGTTGGCTCCTTATGACCCTGACTGGTACTACGTCAGAGCTGGTGAGTTTCTTGTGTTTGATTTTGTGCATTTCCTGGTCCCTTGTTTAAATTAACAAAAAAATAACTTTCGAGGGAACATTTTTTGATCAACCTGTTGTTGAAAATTGCAATGTGTTTTTTGTGCCGCAGCTTCCATGGCCAGGAAGATCTACTTGAGGGGTGGACTCGGTGTTGGTGCATTCCAGAGGATTTATGGTGGAAGTCAGAGAAATGGCAGTCGTCCACCTCATTTCTGCAAGAGCAGTGGTTCCATTGCTCGCCACATTCTTCAACAGTTGCAGAACATGAACCTTATTGAGATGGACACCAAGGGGTAAGAACTCATTATCTTTGTTAGCCTGCTACGGTTTACAATAGGGAATAGGACGATTAAGAGAATAGTAACAATAGATTAGTCAAAGCCGCAATGTAAATCAAATAGTTATTTTAATGTTCACTTGTATCCTGATACCAACATTTGTTGAGCAGTAGTTGATGCTTTTCTGCATCTGTGCTTTTATTTATAGTGATTGGCATTTGCTCAAAAATAGTTTATGCTATTCTGCGTCAGCCCTTCATATCATGTTTTTAACATTGATTTTTCTTTATCACAGTGGCAGGAAGATCACTTCCAGTGGCAGGAGGGATTTGGACCAAGTTGCTGGACGTATTGTTATTGCACCTTGA
Protein sequence

>MS.gene039591.t1

MATARTVQDVSSHEFVKAYSAHLKRSGKMELPEWTDIVKTARFKELAPYDPDWYYVRAASMARKIYLRGGLGVGAFQRIYGGSQRNGSRPPHFCKSSGSIARHILQQLQNMNLIEMDTKGGRKITSSGRRDLDQVAGRIVIAP