AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene83340

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene83340.t1 MTR_2g054750 89.286 140 3 1 1 140 1 128 2.84e-86 248
MS.gene83340.t1 MTR_4g113840 77.857 140 31 0 1 140 1 140 3.55e-80 233
MS.gene83340.t1 MTR_4g011190 45.139 144 60 2 6 134 5 144 3.74e-36 121
MS.gene83340.t1 MTR_3g107610 35.758 165 60 4 6 134 5 159 2.78e-28 102
MS.gene83340.t1 MTR_3g107610 34.014 147 47 4 6 114 5 139 1.34e-19 80.1
MS.gene83340.t1 MTR_3g107610 43.617 94 42 4 50 136 5 94 1.02e-13 65.1
MS.gene83340.t1 MTR_6g069400 28.358 134 74 4 1 134 265 376 5.81e-11 59.3
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene83340.t1 AT2G26695 67.626 139 42 2 1 138 1 137 2.14e-64 193
MS.gene83340.t1 AT2G26695 67.626 139 42 2 1 138 1 137 2.14e-64 193
MS.gene83340.t1 AT5G25490 38.182 165 65 5 6 137 5 165 3.47e-32 112
MS.gene83340.t1 AT5G25490 38.182 165 65 5 6 137 5 165 3.47e-32 112
MS.gene83340.t1 AT3G15680 40.909 154 68 6 6 136 5 158 2.38e-30 107
MS.gene83340.t1 AT3G15680 40.909 154 68 6 6 136 5 158 2.38e-30 107
MS.gene83340.t1 AT2G17975 31.544 149 72 6 6 130 7 149 6.87e-14 67.0
MS.gene83340.t1 AT2G17975 31.507 146 84 6 2 140 125 261 7.32e-11 58.5
MS.gene83340.t1 AT2G17975 31.724 145 83 6 3 140 96 231 2.88e-11 59.3

Find 37 sgRNAs with CRISPR-Local

Find 100 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TCTTAGGGTATCCACAATTT+TGG 0.169674 2.2:+29867571 None:intergenic
CAGTTATATCTATAGGTTTC+TGG 0.204139 2.2:+29867534 None:intergenic
GGATCAGGGCCTCCAATCTT+AGG 0.228355 2.2:+29867555 None:intergenic
ACATTTCATACCAAAACTTT+TGG 0.233482 2.2:+29866720 None:intergenic
AATGGTTACTCTTGTGGATT+TGG 0.299384 2.2:-29867411 MS.gene83340:CDS
ATGGATGCCTCTGGTGGATA+TGG 0.313642 2.2:-29867381 MS.gene83340:CDS
TATCTATAGGTTTCTGGATC+AGG 0.325728 2.2:+29867540 None:intergenic
TGCAAAACACCCAAAAGTTT+TGG 0.338060 2.2:-29866730 MS.gene83340:intron
CAGAAACCTATAGATATAAC+TGG 0.359021 2.2:-29867533 MS.gene83340:CDS
TTCAGTCCAGTTATATCTAT+AGG 0.364972 2.2:+29867527 None:intergenic
TCTTCTTGAAATTTATATGC+TGG 0.441540 2.2:+29867604 None:intergenic
AATTGTGGATACCCTAAGAT+TGG 0.457887 2.2:-29867567 MS.gene83340:CDS
TGAGCTGGTCAGGAGGAGAT+TGG 0.487008 2.2:-29867641 MS.gene83340:CDS
ATCTATAGGTTTCTGGATCA+GGG 0.490676 2.2:+29867541 None:intergenic
GGTGGGAACATGGATGCCTC+TGG 0.491282 2.2:-29867390 MS.gene83340:CDS
ATATAACTGGACTGAAACCT+TGG 0.499509 2.2:-29867520 MS.gene83340:CDS
AACTGGACTGAAACCTTGGC+AGG 0.503471 2.2:-29867516 MS.gene83340:CDS
GATCAGGGCCTCCAATCTTA+GGG 0.508242 2.2:+29867556 None:intergenic
CTGAAACCTTGGCAGGGGAC+TGG 0.517119 2.2:-29867509 MS.gene83340:CDS
CTGGATGGAAAACTGGTGAC+TGG 0.527330 2.2:-29867338 MS.gene83340:CDS
AGCATATAAATTTCAAGAAG+AGG 0.527814 2.2:-29867602 MS.gene83340:CDS
TTGTGGATTTGGTGGGAACA+TGG 0.541127 2.2:-29867400 MS.gene83340:CDS
GGTTACTCTTGTGGATTTGG+TGG 0.558743 2.2:-29867408 MS.gene83340:CDS
GCATATAAATTTCAAGAAGA+GGG 0.572289 2.2:-29867601 MS.gene83340:CDS
CTGGTGACTGGATATGCACT+AGG 0.573750 2.2:-29867326 MS.gene83340:intron
TGTGGATACCCTAAGATTGG+AGG 0.581161 2.2:-29867564 MS.gene83340:CDS
AGGGATGCATGCCAAAATTG+TGG 0.584842 2.2:-29867582 MS.gene83340:CDS
TCATGTATCAGATATGGCTG+TGG 0.590303 2.2:-29866790 MS.gene83340:intron
GTTACTCTTGTGGATTTGGT+GGG 0.590561 2.2:-29867407 MS.gene83340:CDS
GGGAACATGGATGCCTCTGG+TGG 0.591219 2.2:-29867387 MS.gene83340:CDS
ACTGGACTGAAACCTTGGCA+GGG 0.594678 2.2:-29867515 MS.gene83340:CDS
GCAGGGGACTGGTATTGCAG+TGG 0.597750 2.2:-29867498 MS.gene83340:CDS
GCAATACCAGTCCCCTGCCA+AGG 0.605697 2.2:+29867503 None:intergenic
CTGGACTGAAACCTTGGCAG+GGG 0.627405 2.2:-29867514 MS.gene83340:CDS
AGAACAAGCTGTTATAGATG+TGG 0.633263 2.2:-29867444 MS.gene83340:CDS
ATCAGATCCATATCCACCAG+AGG 0.683350 2.2:+29867374 None:intergenic
TATTGCAGTGGTATGAACTG+TGG 0.711677 2.2:-29867486 MS.gene83340:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AATTAATTATATAAGCATCA+TGG + chr2.2:29867621-29867640 None:intergenic 15.0%
!! ATATAATTAATTCCTATTTC+AGG - chr2.2:29867629-29867648 MS.gene83340:CDS 15.0%
!! TAATTACAAAATATGTGATA+GGG + chr2.2:29867175-29867194 None:intergenic 15.0%
!! TTAATTACAAAATATGTGAT+AGG + chr2.2:29867176-29867195 None:intergenic 15.0%
!! AACATATCTATAATTAGACT+TGG - chr2.2:29867260-29867279 MS.gene83340:intron 20.0%
!! ACATATCTATAATTAGACTT+GGG - chr2.2:29867261-29867280 MS.gene83340:intron 20.0%
!! AGTCTAATTATAGATATGTT+TGG + chr2.2:29867260-29867279 None:intergenic 20.0%
!!! ATCACATATTTTGTAATTGA+GGG - chr2.2:29866979-29866998 MS.gene83340:intron 20.0%
! AGCATATAAATTTCAAGAAG+AGG - chr2.2:29866668-29866687 MS.gene83340:intron 25.0%
! CATATCTATAATTAGACTTG+GGG - chr2.2:29867262-29867281 MS.gene83340:intron 25.0%
! GCATATAAATTTCAAGAAGA+GGG - chr2.2:29866669-29866688 MS.gene83340:intron 25.0%
! GCATATACTTTAAGTAATGA+AGG + chr2.2:29867580-29867599 None:intergenic 25.0%
! TAATTAATTCCTATTTCAGG+TGG - chr2.2:29867632-29867651 MS.gene83340:CDS 25.0%
! TCTTCTTGAAATTTATATGC+TGG + chr2.2:29866669-29866688 None:intergenic 25.0%
!! ACATTTCATACCAAAACTTT+TGG + chr2.2:29867553-29867572 None:intergenic 25.0%
!! CATCACATATTTTGTAATTG+AGG - chr2.2:29866978-29866997 MS.gene83340:intron 25.0%
!! CATTTCATACCAAAACTTTT+GGG + chr2.2:29867552-29867571 None:intergenic 25.0%
!! TCACATATTTTGTAATTGAG+GGG - chr2.2:29866980-29866999 MS.gene83340:intron 25.0%
CAGAAACCTATAGATATAAC+TGG - chr2.2:29866737-29866756 MS.gene83340:CDS 30.0%
CAGTTATATCTATAGGTTTC+TGG + chr2.2:29866739-29866758 None:intergenic 30.0%
CGATAAATTTCAAATCTCCT+CGG + chr2.2:29867343-29867362 None:intergenic 30.0%
TTCAGTCCAGTTATATCTAT+AGG + chr2.2:29866746-29866765 None:intergenic 30.0%
TTGAAAAATGGTTACTCTTG+TGG - chr2.2:29866853-29866872 MS.gene83340:intron 30.0%
! CACTAATGACAGTTTTACAA+TGG - chr2.2:29867314-29867333 MS.gene83340:intron 30.0%
! CGAGGAGATTTGAAATTTAT+CGG - chr2.2:29867341-29867360 MS.gene83340:CDS 30.0%
! TTTTGTGTAAAAACAGGGTA+AGG - chr2.2:29867075-29867094 MS.gene83340:intron 30.0%
!!! TTACCCTGTTTTTACACAAA+AGG + chr2.2:29867076-29867095 None:intergenic 30.0%
AATGGTTACTCTTGTGGATT+TGG - chr2.2:29866859-29866878 MS.gene83340:intron 35.0%
AATTGTGGATACCCTAAGAT+TGG - chr2.2:29866703-29866722 MS.gene83340:intron 35.0%
AGAACAAGCTGTTATAGATG+TGG - chr2.2:29866826-29866845 MS.gene83340:intron 35.0%
AGATGTGGTGCATTGAAAAA+TGG - chr2.2:29866841-29866860 MS.gene83340:intron 35.0%
ATATAACTGGACTGAAACCT+TGG - chr2.2:29866750-29866769 MS.gene83340:CDS 35.0%
CATACAATACACCAAATGGT+GGG - chr2.2:29867101-29867120 MS.gene83340:intron 35.0%
CTATAATTAGACTTGGGGAA+CGG - chr2.2:29867267-29867286 MS.gene83340:intron 35.0%
TGCTTCTCATGTATCAGATA+TGG - chr2.2:29867474-29867493 MS.gene83340:CDS 35.0%
! ACAGCCTTTTGTGTAAAAAC+AGG - chr2.2:29867069-29867088 MS.gene83340:intron 35.0%
! ATCTATAGGTTTCTGGATCA+GGG + chr2.2:29866732-29866751 None:intergenic 35.0%
! CAGCCTTTTGTGTAAAAACA+GGG - chr2.2:29867070-29867089 MS.gene83340:intron 35.0%
! TATCTATAGGTTTCTGGATC+AGG + chr2.2:29866733-29866752 None:intergenic 35.0%
! TGCAAAACACCCAAAAGTTT+TGG - chr2.2:29867540-29867559 MS.gene83340:CDS 35.0%
!! TCTTAGGGTATCCACAATTT+TGG + chr2.2:29866702-29866721 None:intergenic 35.0%
!! TGTTTTGCACTTGAAGCATT+CGG + chr2.2:29867529-29867548 None:intergenic 35.0%
AAATATGTGATAGGGCAACC+CGG + chr2.2:29867167-29867186 None:intergenic 40.0%
CAATCTGAACCACCTGAAAT+AGG + chr2.2:29867644-29867663 None:intergenic 40.0%
GCATACAATACACCAAATGG+TGG - chr2.2:29867100-29867119 MS.gene83340:intron 40.0%
GCTGCATACAATACACCAAA+TGG - chr2.2:29867097-29867116 MS.gene83340:intron 40.0%
GTTGTTGTCATGTGACTGTA+AGG - chr2.2:29867025-29867044 MS.gene83340:intron 40.0%
TAAGCATCATGGATCTGATG+AGG + chr2.2:29867610-29867629 None:intergenic 40.0%
TATTGCAGTGGTATGAACTG+TGG - chr2.2:29866784-29866803 MS.gene83340:intron 40.0%
TCATGTATCAGATATGGCTG+TGG - chr2.2:29867480-29867499 MS.gene83340:CDS 40.0%
TTGTAATTGAGGGGTAACCT+TGG - chr2.2:29866989-29867008 MS.gene83340:intron 40.0%
! GTTACTCTTGTGGATTTGGT+GGG - chr2.2:29866863-29866882 MS.gene83340:intron 40.0%
! TTACACAAAAGGCTGTTTCC+AGG + chr2.2:29867065-29867084 None:intergenic 40.0%
!! GTTATTTTATGTCAGCGCAG+AGG + chr2.2:29867391-29867410 None:intergenic 40.0%
AGGGATGCATGCCAAAATTG+TGG - chr2.2:29866688-29866707 MS.gene83340:intron 45.0%
ATCAGATCCATATCCACCAG+AGG + chr2.2:29866899-29866918 None:intergenic 45.0%
GGTTACTCTTGTGGATTTGG+TGG - chr2.2:29866862-29866881 MS.gene83340:intron 45.0%
GTCATGTGACTGTAAGGTCA+CGG - chr2.2:29867031-29867050 MS.gene83340:intron 45.0%
TCATGTGACTGTAAGGTCAC+GGG - chr2.2:29867032-29867051 MS.gene83340:intron 45.0%
TGTGGATACCCTAAGATTGG+AGG - chr2.2:29866706-29866725 MS.gene83340:intron 45.0%
! AGTCACCAGTTTTCCATCCA+GGG + chr2.2:29866933-29866952 None:intergenic 45.0%
! CAGTTTTACAATGGTCTCCG+AGG - chr2.2:29867323-29867342 MS.gene83340:intron 45.0%
!! TTGTGGATTTGGTGGGAACA+TGG - chr2.2:29866870-29866889 MS.gene83340:intron 45.0%
AACTGGACTGAAACCTTGGC+AGG - chr2.2:29866754-29866773 MS.gene83340:CDS 50.0%
ACTGGACTGAAACCTTGGCA+GGG - chr2.2:29866755-29866774 MS.gene83340:CDS 50.0%
ATTGCAATTACCCCCCTGGA+TGG - chr2.2:29866917-29866936 MS.gene83340:intron 50.0%
CAACTTAACCAGTTGCGCCA+AGG + chr2.2:29867009-29867028 None:intergenic 50.0%
CTGGATGGAAAACTGGTGAC+TGG - chr2.2:29866932-29866951 MS.gene83340:intron 50.0%
CTGGTGACTGGATATGCACT+AGG - chr2.2:29866944-29866963 MS.gene83340:intron 50.0%
GATCAGGGCCTCCAATCTTA+GGG + chr2.2:29866717-29866736 None:intergenic 50.0%
TCTGATTGCAATTACCCCCC+TGG - chr2.2:29866913-29866932 MS.gene83340:intron 50.0%
! ATGGATGCCTCTGGTGGATA+TGG - chr2.2:29866889-29866908 MS.gene83340:intron 50.0%
! CAGTCACCAGTTTTCCATCC+AGG + chr2.2:29866934-29866953 None:intergenic 50.0%
! GTCACCAGTTTTCCATCCAG+GGG + chr2.2:29866932-29866951 None:intergenic 50.0%
! TCACCAGTTTTCCATCCAGG+GGG + chr2.2:29866931-29866950 None:intergenic 50.0%
AAGGTCACGGGTTCAAGTCC+TGG - chr2.2:29867044-29867063 MS.gene83340:intron 55.0%
CTGGACTGAAACCTTGGCAG+GGG - chr2.2:29866756-29866775 MS.gene83340:CDS 55.0%
GGATCAGGGCCTCCAATCTT+AGG + chr2.2:29866718-29866737 None:intergenic 55.0%
TACCCCCCTGGATGGAAAAC+TGG - chr2.2:29866925-29866944 MS.gene83340:intron 55.0%
TGAGCTGGTCAGGAGGAGAT+TGG - chr2.2:29866629-29866648 MS.gene83340:intron 55.0%
! CACCAGTTTTCCATCCAGGG+GGG + chr2.2:29866930-29866949 None:intergenic 55.0%
ACTGAAGCTCCCGCATACGC+AGG + chr2.2:29867141-29867160 None:intergenic 60.0%
AGGGGTAACCTTGGCGCAAC+TGG - chr2.2:29866998-29867017 MS.gene83340:intron 60.0%
ATGCGGGAGCTTCAGTGCAC+CGG - chr2.2:29867145-29867164 MS.gene83340:intron 60.0%
CTGAAACCTTGGCAGGGGAC+TGG - chr2.2:29866761-29866780 MS.gene83340:CDS 60.0%
CTGAAGCTCCCGCATACGCA+GGG + chr2.2:29867140-29867159 None:intergenic 60.0%
GCAATACCAGTCCCCTGCCA+AGG + chr2.2:29866770-29866789 None:intergenic 60.0%
GGGAACATGGATGCCTCTGG+TGG - chr2.2:29866883-29866902 MS.gene83340:intron 60.0%
GGTGGGAACATGGATGCCTC+TGG - chr2.2:29866880-29866899 MS.gene83340:intron 60.0%
! GCAGGGGACTGGTATTGCAG+TGG - chr2.2:29866772-29866791 MS.gene83340:CDS 60.0%
AGCTCCCGCATACGCAGGGT+CGG + chr2.2:29867136-29867155 None:intergenic 65.0%
CATACGCAGGGTCGGGGAAG+GGG + chr2.2:29867128-29867147 None:intergenic 65.0%
CTTCCCCGACCCTGCGTATG+CGG - chr2.2:29867128-29867147 MS.gene83340:intron 65.0%
GCATACGCAGGGTCGGGGAA+GGG + chr2.2:29867129-29867148 None:intergenic 65.0%
GGGGAAGGGGTCCCACCATT+TGG + chr2.2:29867115-29867134 None:intergenic 65.0%
TGCGGGAGCTTCAGTGCACC+GGG - chr2.2:29867146-29867165 MS.gene83340:intron 65.0%
TTCCCCGACCCTGCGTATGC+GGG - chr2.2:29867129-29867148 MS.gene83340:intron 65.0%
CGCATACGCAGGGTCGGGGA+AGG + chr2.2:29867130-29867149 None:intergenic 70.0%
CTCCCGCATACGCAGGGTCG+GGG + chr2.2:29867134-29867153 None:intergenic 70.0%
GCTCCCGCATACGCAGGGTC+GGG + chr2.2:29867135-29867154 None:intergenic 70.0%


Chromosome Type Strat End Strand Name
chr2.2 gene 29866628 29867664 29866628 ID=MS.gene83340
chr2.2 mRNA 29866628 29867664 29866628 ID=MS.gene83340.t1;Parent=MS.gene83340
chr2.2 exon 29867327 29867664 29867327 ID=MS.gene83340.t1.exon1;Parent=MS.gene83340.t1
chr2.2 CDS 29867327 29867664 29867327 ID=cds.MS.gene83340.t1;Parent=MS.gene83340.t1
chr2.2 exon 29866731 29866801 29866731 ID=MS.gene83340.t1.exon2;Parent=MS.gene83340.t1
chr2.2 CDS 29866731 29866801 29866731 ID=cds.MS.gene83340.t1;Parent=MS.gene83340.t1
chr2.2 exon 29866628 29866641 29866628 ID=MS.gene83340.t1.exon3;Parent=MS.gene83340.t1
chr2.2 CDS 29866628 29866641 29866628 ID=cds.MS.gene83340.t1;Parent=MS.gene83340.t1
Gene Sequence

>MS.gene83340

ATGAGCTGGTCAGGAGGAGATTGGATGTGCAATGCTTGCCAGCATATAAATTTCAAGAAGAGGGATGCATGCCAAAATTGTGGATACCCTAAGATTGGAGGCCCTGATCCAGAAACCTATAGATATAACTGGACTGAAACCTTGGCAGGGGACTGGTATTGCAGTGGTATGAACTGTGGAGCTCACAATTATGCTAGCAGAACAAGCTGTTATAGATGTGGTGCATTGAAAAATGGTTACTCTTGTGGATTTGGTGGGAACATGGATGCCTCTGGTGGATATGGATCTGATTGCAATTACCCCCCTGGATGGAAAACTGGTGACTGGATATGCACTAGGTATTTTCACATCATCACATATTTTGTAATTGAGGGGTAACCTTGGCGCAACTGGTTAAGTTGTTGTCATGTGACTGTAAGGTCACGGGTTCAAGTCCTGGAAACAGCCTTTTGTGTAAAAACAGGGTAAGGCTGCATACAATACACCAAATGGTGGGACCCCTTCCCCGACCCTGCGTATGCGGGAGCTTCAGTGCACCGGGTTGCCCTATCACATATTTTGTAATTAACTTCACTAAAATATGCTGCATTTTCATGTACTGAAGTTGCTTTGCAAATTGCAACTACAAACCAAACATATCTATAATTAGACTTGGGGAACGGAGAAATTATTATTAATAAGAATGACACTAATGACAGTTTTACAATGGTCTCCGAGGAGATTTGAAATTTATCGGTTAAAACTACAAAGTCAACTCTCACCTCTGCGCTGACATAAAATAACTCGTTTCATTGTATTACATAAAAAGAAATATGAAATATCATAGAAATACATTTTTATTTTCTTTGCTTCTCATGTATCAGATATGGCTGTGGAGTGCACAATTATGCTAGCAGAGCCGAATGCTTCAAGTGCAAAACACCCAAAAGTTTTGGTATGAAATGTTTATCCTTCATTACTTAAAGTATATGCTATTCAACCTCATCAGATCCATGATGCTTATATAATTAATTCCTATTTCAGGTGGTTCAGATTGA
Protein sequence

>MS.gene83340.t1

MSWSGGDWMCNACQHINFKKRDACQNCGYPKIGGPDPETYRYNWTETLAGDWYCSGMNCGAHNYASRTSCYRCGALKNGYSCGFGGNMDASGGYGSDCNYPPGWKTGDWICTRYGCGVHNYASRAECFKCKTPKSFGGSD