AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene064025


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene064025.t1 MTR_6g090515 96.335 191 7 0 1 191 30 220 1.69e-130 365
MS.gene064025.t1 MTR_8g102030 85.864 191 25 2 1 191 34 222 1.34e-93 272
MS.gene064025.t1 MTR_8g102020 72.775 191 35 2 1 191 32 205 1.37e-71 216
MS.gene064025.t1 MTR_1g090490 30.000 180 107 4 4 165 36 214 3.34e-13 65.9
MS.gene064025.t1 MTR_1g090490 30.000 180 107 4 4 165 36 214 3.43e-13 66.2
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene064025.t1 AT2G19830 83.854 192 23 3 1 191 10 194 1.71e-97 281
MS.gene064025.t1 AT2G19830 83.854 192 23 3 1 191 29 213 3.00e-97 281
MS.gene064025.t1 AT4G29160 86.667 180 23 1 13 191 13 192 3.21e-96 277
MS.gene064025.t1 AT4G29160 86.667 180 23 1 13 191 40 219 1.03e-95 277
MS.gene064025.t1 AT4G29160 86.667 180 23 1 13 191 40 219 1.03e-95 277
MS.gene064025.t1 AT5G04850 30.935 139 88 1 10 140 35 173 3.02e-12 63.5
MS.gene064025.t1 AT3G10640 30.220 182 101 4 10 165 35 216 1.01e-11 62.0
MS.gene064025.t1 AT3G10640 30.488 164 93 4 33 175 1 164 6.22e-11 58.9
MS.gene064025.t1 AT5G09260 31.250 144 94 2 15 157 41 180 8.70e-11 59.3

Find 43 sgRNAs with CRISPR-Local

Find 83 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ACTAGAAATGCTTGAGAAAA+AGG 0.221659 6.1:-79187969 None:intergenic
TCCTCAGGAGTCGGCTTTGC+AGG 0.229972 6.1:+79186639 None:intergenic
AGATGAATTGGCAGCTTTGC+AGG 0.277136 6.1:-79186616 MS.gene064025:CDS
TTGAATCTGCTTCATGTTCT+CGG 0.295683 6.1:+79187340 None:intergenic
GGAAAATGTACTCCTTAAAA+AGG 0.296574 6.1:-79187948 MS.gene064025:CDS
CACCAAAAGAAAGAACAAAA+AGG 0.308755 6.1:-79187894 MS.gene064025:CDS
GGAAGCAGAACTTGAAGAAT+TGG 0.338385 6.1:-79186760 MS.gene064025:CDS
CCCACAGTGCATGTCCCAGC+TGG 0.344057 6.1:-79186684 MS.gene064025:CDS
CGTGCAGGTTGCCTCCCAGC+TGG 0.353565 6.1:+79186669 None:intergenic
GGAGTCGGCTTTGCAGGAAC+AGG 0.397015 6.1:+79186645 None:intergenic
GACTCCTGAGGAAGATGAAT+TGG 0.412289 6.1:-79186628 MS.gene064025:CDS
TTGTTCTTTACAGGACGAAT+TGG 0.437007 6.1:-79186781 MS.gene064025:intron
GGAGCAGGAGCTGTAGTTGC+TGG 0.442696 6.1:+79186705 None:intergenic
AAATCAGCAGCTGCACCAAT+TGG 0.448641 6.1:+79187302 None:intergenic
TAATAGATGATAATGTTAGA+AGG 0.453601 6.1:-79187594 MS.gene064025:intron
CCAGTTGCGTATTCATGACC+AGG 0.454482 6.1:-79187701 MS.gene064025:intron
CCAGCTGGGACATGCACTGT+GGG 0.462898 6.1:+79186684 None:intergenic
GCAGATTCAAGAAGCATTGT+CGG 0.464581 6.1:-79187327 MS.gene064025:CDS
AGAATTGGAGAGTGCTGAGT+TGG 0.466125 6.1:-79186745 MS.gene064025:CDS
ACGGTAGATGCGTTAAGAAC+AGG 0.469044 6.1:-79187552 MS.gene064025:CDS
TTCAATGTTTGAAGAGGAAG+AGG 0.475427 6.1:-79187759 MS.gene064025:CDS
TGCTAAAGCCACCACGGAAA+CGG 0.478535 6.1:-79187571 MS.gene064025:CDS
CCTGGTCATGAATACGCAAC+TGG 0.481018 6.1:+79187701 None:intergenic
GGGACATGCACTGTGGGAGC+AGG 0.482842 6.1:+79186690 None:intergenic
GAAGCATTGTCGGCTCCAAT+TGG 0.484568 6.1:-79187317 MS.gene064025:CDS
CGCATCTACCGTTTCCGTGG+TGG 0.487516 6.1:+79187563 None:intergenic
GGCAGCTTTGCAGGCTGAGA+TGG 0.492052 6.1:-79186607 MS.gene064025:CDS
TTTGCAGGAACAGGGCGTGC+AGG 0.497715 6.1:+79186654 None:intergenic
CTGTTCATTTATCTCGTCCA+TGG 0.501356 6.1:+79187364 None:intergenic
CCACAGTGCATGTCCCAGCT+GGG 0.512082 6.1:-79186683 MS.gene064025:CDS
GCTGCCAATTCATCTTCCTC+AGG 0.526016 6.1:+79186624 None:intergenic
AATTCATCTTCCTCAGGAGT+CGG 0.548839 6.1:+79186630 None:intergenic
GTGCAGGTTGCCTCCCAGCT+GGG 0.551247 6.1:+79186670 None:intergenic
CGGCAATTCAATGTTTGAAG+AGG 0.561917 6.1:-79187765 MS.gene064025:CDS
CCCAGCTGGGACATGCACTG+TGG 0.570484 6.1:+79186683 None:intergenic
AACAGGAGCAGCTACTATGA+AGG 0.577122 6.1:-79187535 MS.gene064025:CDS
TAACGCATCTACCGTTTCCG+TGG 0.584559 6.1:+79187560 None:intergenic
GAACAACAAGTTGAGCAGCT+TGG 0.596454 6.1:-79187730 MS.gene064025:CDS
GAGTCGGCTTTGCAGGAACA+GGG 0.596697 6.1:+79186646 None:intergenic
TCCTGCAAAGCCGACTCCTG+AGG 0.597589 6.1:-79186640 MS.gene064025:CDS
CAGTGCATGTCCCAGCTGGG+AGG 0.671305 6.1:-79186680 MS.gene064025:CDS
TGATGACGTTGACAAGACCA+TGG 0.678474 6.1:-79187381 MS.gene064025:CDS
AGAAGGTGCTAAAGCCACCA+CGG 0.700426 6.1:-79187577 MS.gene064025:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAATGCTTATTTATTTATGT+TGG - chr6.1:79187300-79187319 MS.gene064025:CDS 15.0%
!! ATGATTTATTTAATTGAGTT+TGG - chr6.1:79187133-79187152 MS.gene064025:intron 15.0%
!!! TCATTTTCTTAAAATATGAT+TGG + chr6.1:79187634-79187653 None:intergenic 15.0%
!! TTGATTACGTAAAAAAAATG+AGG + chr6.1:79187476-79187495 None:intergenic 20.0%
!!! CTTTTCACTTAATTTTGTTT+TGG - chr6.1:79187524-79187543 MS.gene064025:CDS 20.0%
!!! TAATAGATGATAATGTTAGA+AGG - chr6.1:79186967-79186986 MS.gene064025:intron 20.0%
!!! TTTAGTATTAGTTTAGACAA+TGG - chr6.1:79186899-79186918 MS.gene064025:intron 20.0%
! AATAAATTCAGAATGCTACA+CGG + chr6.1:79187762-79187781 None:intergenic 25.0%
! ACCAAAAGAAAGAACAAAAA+GGG - chr6.1:79186668-79186687 MS.gene064025:CDS 25.0%
! ATATACAAAACACTAATGCA+TGG - chr6.1:79187605-79187624 MS.gene064025:intron 25.0%
! CTGAATTTATTGTTCTTTAC+AGG - chr6.1:79187771-79187790 MS.gene064025:intron 25.0%
! TTCTAATTTCACTTAATCCA+TGG - chr6.1:79186744-79186763 MS.gene064025:CDS 25.0%
! TTTGTATATAAGTACTACTC+TGG + chr6.1:79187594-79187613 None:intergenic 25.0%
!! GTTTGATTATTTGTACCTTT+TGG - chr6.1:79187336-79187355 MS.gene064025:CDS 25.0%
AAAGAAAGAACAAAAAGGGT+AGG - chr6.1:79186672-79186691 MS.gene064025:CDS 30.0%
CACCAAAAGAAAGAACAAAA+AGG - chr6.1:79186667-79186686 MS.gene064025:CDS 30.0%
CTACTCTGGACTTAAAATAT+AGG + chr6.1:79187580-79187599 None:intergenic 30.0%
GGAAAATGTACTCCTTAAAA+AGG - chr6.1:79186613-79186632 MS.gene064025:CDS 30.0%
TTCAGACAGATTACGAAAAA+TGG - chr6.1:79187446-79187465 MS.gene064025:intron 30.0%
TTGAATGTAACCACATGTAT+CGG - chr6.1:79187659-79187678 MS.gene064025:intron 30.0%
! ACCCTTTTTGTTCTTTCTTT+TGG + chr6.1:79186672-79186691 None:intergenic 30.0%
!! CTTTCTTTTGGTGTATTCTT+TGG + chr6.1:79186660-79186679 None:intergenic 30.0%
!!! TGATTTTTTGTTTTACGCAG+CGG - chr6.1:79186776-79186795 MS.gene064025:intron 30.0%
AAAAATCAAGTCACGTTCCA+TGG + chr6.1:79186764-79186783 None:intergenic 35.0%
CTTCAGATTGAACACATGTT+CGG + chr6.1:79187706-79187725 None:intergenic 35.0%
TTCAATGTTTGAAGAGGAAG+AGG - chr6.1:79186802-79186821 MS.gene064025:intron 35.0%
TTGAATCTGCTTCATGTTCT+CGG + chr6.1:79187224-79187243 None:intergenic 35.0%
TTGTTCTTTACAGGACGAAT+TGG - chr6.1:79187780-79187799 MS.gene064025:intron 35.0%
! AAACTCTGAAGAACAAGTAG+AGG + chr6.1:79186717-79186736 None:intergenic 35.0%
! ATGTGTTCAATCTGAAGTGT+TGG - chr6.1:79187709-79187728 MS.gene064025:CDS 35.0%
! TAATCTTCTTTTGCGTCTTC+TGG - chr6.1:79186932-79186951 MS.gene064025:intron 35.0%
!! TTGGTTCTGTTTCTTTCTAC+AGG - chr6.1:79187152-79187171 MS.gene064025:intron 35.0%
AATACAACTGTGTTCACACC+TGG + chr6.1:79186881-79186900 None:intergenic 40.0%
AATTCATCTTCCTCAGGAGT+CGG + chr6.1:79187934-79187953 None:intergenic 40.0%
AGTGCTGTACAATACTCTCT+CGG - chr6.1:79187367-79187386 MS.gene064025:CDS 40.0%
CAGCACTATACACAACCAAA+AGG + chr6.1:79187354-79187373 None:intergenic 40.0%
CGGCAATTCAATGTTTGAAG+AGG - chr6.1:79186796-79186815 MS.gene064025:intron 40.0%
CTGTTCATTTATCTCGTCCA+TGG + chr6.1:79187200-79187219 None:intergenic 40.0%
GGAAGCAGAACTTGAAGAAT+TGG - chr6.1:79187801-79187820 MS.gene064025:intron 40.0%
TGTACTCCTTAAAAAGGCCA+CGG - chr6.1:79186619-79186638 MS.gene064025:CDS 40.0%
!! GCAGATTCAAGAAGCATTGT+CGG - chr6.1:79187234-79187253 MS.gene064025:intron 40.0%
!! TGTTCAATCTGAAGTGTTGG+TGG - chr6.1:79187712-79187731 MS.gene064025:CDS 40.0%
AAATCAGCAGCTGCACCAAT+TGG + chr6.1:79187262-79187281 None:intergenic 45.0%
AACAGGAGCAGCTACTATGA+AGG - chr6.1:79187026-79187045 MS.gene064025:intron 45.0%
ACGGTAGATGCGTTAAGAAC+AGG - chr6.1:79187009-79187028 MS.gene064025:intron 45.0%
AGATGAATTGGCAGCTTTGC+AGG - chr6.1:79187945-79187964 MS.gene064025:CDS 45.0%
GACTCCTGAGGAAGATGAAT+TGG - chr6.1:79187933-79187952 MS.gene064025:CDS 45.0%
GTGCTGTACAATACTCTCTC+GGG - chr6.1:79187368-79187387 MS.gene064025:CDS 45.0%
! GAACAACAAGTTGAGCAGCT+TGG - chr6.1:79186831-79186850 MS.gene064025:intron 45.0%
! TCTTCTTTTGCGTCTTCTGG+TGG - chr6.1:79186935-79186954 MS.gene064025:intron 45.0%
! TGATGACGTTGACAAGACCA+TGG - chr6.1:79187180-79187199 MS.gene064025:intron 45.0%
!! AAGTGTTGGTGGTGCTACAT+TGG - chr6.1:79187723-79187742 MS.gene064025:CDS 45.0%
!! AGAATTGGAGAGTGCTGAGT+TGG - chr6.1:79187816-79187835 MS.gene064025:intron 45.0%
!! CAATACAGTGCCGATACATG+TGG + chr6.1:79187672-79187691 None:intergenic 45.0%
ATCGGCACTGTATTGCGTGT+CGG - chr6.1:79187677-79187696 MS.gene064025:intron 50.0%
CCAGTTGCGTATTCATGACC+AGG - chr6.1:79186860-79186879 MS.gene064025:intron 50.0%
CCTGGTCATGAATACGCAAC+TGG + chr6.1:79186863-79186882 None:intergenic 50.0%
GCTGCCAATTCATCTTCCTC+AGG + chr6.1:79187940-79187959 None:intergenic 50.0%
TAACGCATCTACCGTTTCCG+TGG + chr6.1:79187004-79187023 None:intergenic 50.0%
TGCTAAAGCCACCACGGAAA+CGG - chr6.1:79186990-79187009 MS.gene064025:intron 50.0%
! CTTCTGCCGTGGCCTTTTTA+AGG + chr6.1:79186628-79186647 None:intergenic 50.0%
! TCTTTTGCGTCTTCTGGTGG+TGG - chr6.1:79186938-79186957 MS.gene064025:intron 50.0%
!! AGAAGGTGCTAAAGCCACCA+CGG - chr6.1:79186984-79187003 MS.gene064025:intron 50.0%
!! GAAGCATTGTCGGCTCCAAT+TGG - chr6.1:79187244-79187263 MS.gene064025:intron 50.0%
!! TGTTGGTGGTGCTACATTGG+TGG - chr6.1:79187726-79187745 MS.gene064025:CDS 50.0%
!!! GGCTTTTTCAACTTCTGCCG+TGG + chr6.1:79186639-79186658 None:intergenic 50.0%
!!! TGCAGCTGCTGATTTTGACG+AGG - chr6.1:79187267-79187286 MS.gene064025:intron 50.0%
! GAGTCGGCTTTGCAGGAACA+GGG + chr6.1:79187918-79187937 None:intergenic 55.0%
CCACAGTGCATGTCCCAGCT+GGG - chr6.1:79187878-79187897 MS.gene064025:intron 60.0%
CCAGCTGGGACATGCACTGT+GGG + chr6.1:79187880-79187899 None:intergenic 60.0%
CGCATCTACCGTTTCCGTGG+TGG + chr6.1:79187001-79187020 None:intergenic 60.0%
GGAGCAGGAGCTGTAGTTGC+TGG + chr6.1:79187859-79187878 None:intergenic 60.0%
GGCAGCTTTGCAGGCTGAGA+TGG - chr6.1:79187954-79187973 MS.gene064025:CDS 60.0%
TTTGCAGGAACAGGGCGTGC+AGG + chr6.1:79187910-79187929 None:intergenic 60.0%
! GGAGTCGGCTTTGCAGGAAC+AGG + chr6.1:79187919-79187938 None:intergenic 60.0%
! TCCTCAGGAGTCGGCTTTGC+AGG + chr6.1:79187925-79187944 None:intergenic 60.0%
! TCCTGCAAAGCCGACTCCTG+AGG - chr6.1:79187921-79187940 MS.gene064025:CDS 60.0%
CAGTGCATGTCCCAGCTGGG+AGG - chr6.1:79187881-79187900 MS.gene064025:intron 65.0%
CCCACAGTGCATGTCCCAGC+TGG - chr6.1:79187877-79187896 MS.gene064025:intron 65.0%
CCCAGCTGGGACATGCACTG+TGG + chr6.1:79187881-79187900 None:intergenic 65.0%
GGGACATGCACTGTGGGAGC+AGG + chr6.1:79187874-79187893 None:intergenic 65.0%
GTGCAGGTTGCCTCCCAGCT+GGG + chr6.1:79187894-79187913 None:intergenic 65.0%
CGTGCAGGTTGCCTCCCAGC+TGG + chr6.1:79187895-79187914 None:intergenic 70.0%


Chromosome Type Strat End Strand Name
chr6.1 gene 79186599 79187984 79186599 ID=MS.gene064025
chr6.1 mRNA 79186599 79187984 79186599 ID=MS.gene064025.t1;Parent=MS.gene064025
chr6.1 exon 79187894 79187984 79187894 ID=MS.gene064025.t1.exon1;Parent=MS.gene064025.t1
chr6.1 CDS 79187894 79187984 79187894 ID=cds.MS.gene064025.t1;Parent=MS.gene064025.t1
chr6.1 exon 79187702 79187787 79187702 ID=MS.gene064025.t1.exon2;Parent=MS.gene064025.t1
chr6.1 CDS 79187702 79187787 79187702 ID=cds.MS.gene064025.t1;Parent=MS.gene064025.t1
chr6.1 exon 79187519 79187610 79187519 ID=MS.gene064025.t1.exon3;Parent=MS.gene064025.t1
chr6.1 CDS 79187519 79187610 79187519 ID=cds.MS.gene064025.t1;Parent=MS.gene064025.t1
chr6.1 exon 79187295 79187409 79187295 ID=MS.gene064025.t1.exon4;Parent=MS.gene064025.t1
chr6.1 CDS 79187295 79187409 79187295 ID=cds.MS.gene064025.t1;Parent=MS.gene064025.t1
chr6.1 exon 79186599 79186790 79186599 ID=MS.gene064025.t1.exon5;Parent=MS.gene064025.t1
chr6.1 CDS 79186599 79186790 79186599 ID=cds.MS.gene064025.t1;Parent=MS.gene064025.t1
Gene Sequence

>MS.gene064025

ATGCTTGAGAAAAAGGAAAATGTACTCCTTAAAAAGGCCACGGCAGAAGTTGAAAAAGCCAAAGAATACACCAAAAGAAAGAACAAAAAGGGTAGGTTGCTAGCTTAACTGAACTCCTCTACTTGTTCTTCAGAGTTTTCTTTAATTCTAATTTCACTTAATCCATGGAACGTGACTTGATTTTTTGTTTTACGCAGCGGCAATTCAATGTTTGAAGAGGAAGAGGTTATATGAACAACAAGTTGAGCAGCTTGGTAATTTCCAGTTGCGTATTCATGACCAGGTGTGAACACAGTTGTATTTAGTATTAGTTTAGACAATGGTTTAGAATATTAATCTTCTTTTGCGTCTTCTGGTGGTGGTTTTTGTAATAGATGATAATGTTAGAAGGTGCTAAAGCCACCACGGAAACGGTAGATGCGTTAAGAACAGGAGCAGCTACTATGAAGGCTATGCAGAAAGCAACGTATGTATTGCTATTATATACGATATATGATTCTAAGTCTTCAACAATCGAGCTGTTGATTATGATTTATGATTTATTTAATTGAGTTTGGTTCTGTTTCTTTCTACAGGAATATTGATGACGTTGACAAGACCATGGACGAGATAAATGAACAGACCGAGAACATGAAGCAGATTCAAGAAGCATTGTCGGCTCCAATTGGTGCAGCTGCTGATTTTGACGAGGTTATTCTCTCAAATGCTTATTTATTTATGTTGGTTGAAAACACAATGTTTGATTATTTGTACCTTTTGGTTGTGTATAGTGCTGTACAATACTCTCTCGGGACTCAATTATAAAGCAAAAAAAAAATATAATAAAAAATAATAAAAAAATACTAATTTCAGACAGATTACGAAAAATGGTTAACCTCATTTTTTTTACGTAATCAAAAAAAATACTCTCTTTTCTAAATACTCTCTTTTCACTTAATTTTGTTTTGGAACATAATTAATTGAATTAGTTAGATTTTGCCTATATTTTAAGTCCAGAGTAGTACTTATATACAAAACACTAATGCATGGACACCAATCATATTTTAAGAAAATGAAGTGATTGAATGTAACCACATGTATCGGCACTGTATTGCGTGTCGGACTCCGAACATGTGTTCAATCTGAAGTGTTGGTGGTGCTACATTGGTGGTAATGCATTTCCGTGTAGCATTCTGAATTTATTGTTCTTTACAGGACGAATTGGAAGCAGAACTTGAAGAATTGGAGAGTGCTGAGTTGGAAGAACAGCTTCTTCAGCCAGCAACTACAGCTCCTGCTCCCACAGTGCATGTCCCAGCTGGGAGGCAACCTGCACGCCCTGTTCCTGCAAAGCCGACTCCTGAGGAAGATGAATTGGCAGCTTTGCAGGCTGAGATGGCACTTTGA

Protein sequence

>MS.gene064025.t1

MLEKKENVLLKKATAEVEKAKEYTKRKNKKAAIQCLKRKRLYEQQVEQLGNFQLRIHDQMIMLEGAKATTETVDALRTGAATMKAMQKATNIDDVDKTMDEINEQTENMKQIQEALSAPIGAAADFDEDELEAELEELESAELEEQLLQPATTAPAPTVHVPAGRQPARPVPAKPTPEEDELAALQAEMAL