AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar ZhongmuNo.1 / MsG0280011210.01

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0280011210.01.T01 MTR_2g100060 75.314 239 34 4 15 228 22 260 2.87e-113 325
MsG0280011210.01.T01 MTR_8g016370 45.291 223 110 6 8 228 13 225 8.69e-59 185
MsG0280011210.01.T01 MTR_3g104460 36.680 259 122 9 3 227 9 259 3.28e-46 154
MsG0280011210.01.T01 MTR_5g087760 28.289 152 83 4 67 192 80 231 3.61e-13 67.0
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0280011210.01.T01 AT1G17620 39.919 248 116 6 12 227 17 263 1.07e-41 142
MsG0280011210.01.T01 AT5G11890 30.038 263 132 10 5 227 36 286 3.55e-28 108
MsG0280011210.01.T01 AT5G36970 29.651 172 92 7 75 223 83 248 6.84e-11 60.8

Find 75 sgRNAs with CRISPR-Local

Find 86 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTCGAAGTTGACGCCGTTAC+TGG 0.277675 2:+80990349 None:intergenic
GCTGCTGCACCTTCTTCTTC+TGG 0.279365 2:-80990881 MsG0280011210.01.T01:CDS
TCCTTTCTCCTCGGCGTAAC+GGG 0.321623 2:-80990836 MsG0280011210.01.T01:CDS
ACGAAGGTGATATGTTTGTT+AGG 0.332211 2:+80990681 None:intergenic
TGCTTGACCAGTACTCAAAA+TGG 0.356336 2:+80990551 None:intergenic
CGAAGGTGATATGTTTGTTA+GGG 0.379442 2:+80990682 None:intergenic
CTTCATCAATTAAATTTAAA+CGG 0.385881 2:+80990282 None:intergenic
TGAGTTGAGGGTGGAGGAGG+AGG 0.397719 2:+80990734 None:intergenic
TTGATGTTAGGTTTAAGATC+TGG 0.438319 2:-80990312 MsG0280011210.01.T01:CDS
TGAGGGTGGAGGAGGAGGTG+AGG 0.440148 2:+80990739 None:intergenic
CTCCTTTCTCCTCGGCGTAA+CGG 0.440415 2:-80990837 MsG0280011210.01.T01:CDS
CAACGGCGGCGGTACGGCGG+TGG 0.445693 2:+80990903 None:intergenic
TTAAGTGTGATGTTGATGTT+AGG 0.446188 2:-80990324 MsG0280011210.01.T01:CDS
TTTAGCGTTGAAAGTGAAGT+TGG 0.454211 2:-80990475 MsG0280011210.01.T01:intron
TGAGGTTGTGGACGGTAGGT+AGG 0.457022 2:+80990926 None:intergenic
TTCTCATCCTCCTTTCTCCT+CGG 0.459714 2:-80990845 MsG0280011210.01.T01:CDS
CAGCAGCAACGGCGGCGGTA+CGG 0.462778 2:+80990897 None:intergenic
GTACGGCGGTGGTGAGGTTG+TGG 0.465045 2:+80990914 None:intergenic
CAGCAACGGCGGCGGTACGG+CGG 0.467451 2:+80990900 None:intergenic
GTAACTCTTATTCCAACGTT+AGG 0.471241 2:+80990415 None:intergenic
GGCTGGAAATGATGGGTTTG+CGG 0.475941 2:+80990979 None:intergenic
AGAAGAAGGTGCAGCAGCAA+CGG 0.479402 2:+80990886 None:intergenic
TTAGGTTTAAGATCTGGAAA+TGG 0.481195 2:-80990306 MsG0280011210.01.T01:CDS
AAAGGAGGATGAGAAGTATG+AGG 0.482516 2:+80990853 None:intergenic
TTCTTGCCATGTGTGAAAGT+TGG 0.485690 2:+80990597 None:intergenic
GACACCGTTGCCGTTGGTCA+TGG 0.490825 2:+80991030 None:intergenic
GAGAGAATTGTGATGGTGGT+TGG 0.496275 2:+80990651 None:intergenic
GAGGTTGTGGACGGTAGGTA+GGG 0.503122 2:+80990927 None:intergenic
GCCCGTTACGCCGAGGAGAA+AGG 0.506329 2:+80990835 None:intergenic
ACTGGTTTCTTATTACCGAC+AGG 0.516093 2:+80990367 None:intergenic
AGGTGCAGCAGCAACGGCGG+CGG 0.517857 2:+80990892 None:intergenic
GTTTGAGAGAATTGTGATGG+TGG 0.523617 2:+80990647 None:intergenic
TTGTGGACGGTAGGTAGGGC+GGG 0.525214 2:+80990931 None:intergenic
GCGGCGGTACGGCGGTGGTG+AGG 0.527425 2:+80990908 None:intergenic
GCCATGTGTGAAAGTTGGTA+TGG 0.529809 2:+80990602 None:intergenic
GTTGTGGACGGTAGGTAGGG+CGG 0.531506 2:+80990930 None:intergenic
GCCACAAAAGCTCAACTCTA+CGG 0.539658 2:-80990959 MsG0280011210.01.T01:CDS
GTGGTGAGGTTGTGGACGGT+AGG 0.539763 2:+80990922 None:intergenic
GTTGTTTGAGAGAATTGTGA+TGG 0.543870 2:+80990644 None:intergenic
ATACAAAGTGAAGGCTAAAG+TGG 0.552779 2:-80990452 MsG0280011210.01.T01:CDS
GAGAGATGTTACGGTGAGGA+AGG 0.555294 2:+80990779 None:intergenic
AACGGTGTCACCAACGGTAA+CGG 0.557429 2:-80991016 MsG0280011210.01.T01:CDS
TTACGGTGAGGAAGGACGGT+GGG 0.562791 2:+80990787 None:intergenic
GTGAGGAAGGACGGTGGGGA+CGG 0.564474 2:+80990792 None:intergenic
GTCACCAACGGTAACGGTAA+CGG 0.571662 2:-80991010 MsG0280011210.01.T01:CDS
GTTGGTGACACCGTTGCCGT+TGG 0.575232 2:+80991024 None:intergenic
GACGGTGGGGACGGTAGATG+AGG 0.578731 2:+80990801 None:intergenic
AACGGCAACGGTGTCACCAA+CGG 0.582278 2:-80991022 MsG0280011210.01.T01:CDS
AGAAGGTGCAGCAGCAACGG+CGG 0.583077 2:+80990889 None:intergenic
ATTAGAATCAGACGCTTCCA+CGG 0.587238 2:-80990529 MsG0280011210.01.T01:CDS
GAATTGTGATGGTGGTTGGT+TGG 0.587560 2:+80990655 None:intergenic
CATGTTCTTCTTCAGCTCCG+TGG 0.589253 2:+80990512 None:intergenic
GTTAGAGTTCATGTTCCTGT+CGG 0.590463 2:-80990382 MsG0280011210.01.T01:CDS
TACAAAGTGAAGGCTAAAGT+GGG 0.593252 2:-80990451 MsG0280011210.01.T01:CDS
GAGGAAGAACCAGAAGAAGA+AGG 0.593450 2:+80990872 None:intergenic
AACAACATCAACATCGGTGA+AGG 0.594037 2:-80990627 MsG0280011210.01.T01:CDS
AAAACCATGACCAACGGCAA+CGG 0.594643 2:-80991034 None:intergenic
GATGTTACGGTGAGGAAGGA+CGG 0.597094 2:+80990783 None:intergenic
AAAATGAAAACACCTAACGT+TGG 0.600696 2:-80990427 MsG0280011210.01.T01:CDS
TGGACGGTAGGTAGGGCGGG+TGG 0.609236 2:+80990934 None:intergenic
CTCTCAAACAACATCAACAT+CGG 0.615638 2:-80990633 MsG0280011210.01.T01:CDS
GCCGCCAAAACCATGACCAA+CGG 0.616106 2:-80991040 None:intergenic
GACACCGTTACCGTTACCGT+TGG 0.628131 2:+80991006 None:intergenic
GGAATAAGAGTTACATGTGA+CGG 0.629815 2:-80990406 MsG0280011210.01.T01:CDS
GGCGGTGGTGAGGTTGTGGA+CGG 0.633011 2:+80990918 None:intergenic
TGAAGTTGGATACAAAGTGA+AGG 0.636316 2:-80990461 MsG0280011210.01.T01:CDS
TACGGTGAGGAAGGACGGTG+GGG 0.637208 2:+80990788 None:intergenic
TGGAAATGATGGGTTTGCGG+CGG 0.637844 2:+80990982 None:intergenic
ACCATACCAACTTTCACACA+TGG 0.645797 2:-80990603 MsG0280011210.01.T01:CDS
GTTACGGTGAGGAAGGACGG+TGG 0.666551 2:+80990786 None:intergenic
CGTTACGCCGAGGAGAAAGG+AGG 0.671818 2:+80990838 None:intergenic
CGGTAATAAGAAACCAGTAA+CGG 0.676522 2:-80990362 MsG0280011210.01.T01:CDS
AAGCGGTGCCCGTTACGCCG+AGG 0.677693 2:+80990828 None:intergenic
ACGGTAGATGAGGTAGAAAG+CGG 0.681553 2:+80990811 None:intergenic
GGTGGTTGGTTGGTAAACGA+AGG 0.694931 2:+80990665 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
AAAATGAAAACACCTAACGT+TGG - Chr2:80990898-80990917 MsG0280011210.01.T01:CDS 30.0%
AAGAACATGAAGAGCAAAAA+CGG - Chr2:80990827-80990846 MsG0280011210.01.T01:CDS 30.0%
TTAAGTGTGATGTTGATGTT+AGG - Chr2:80991001-80991020 MsG0280011210.01.T01:CDS 30.0%
! TTAGGTTTAAGATCTGGAAA+TGG - Chr2:80991019-80991038 MsG0280011210.01.T01:CDS 30.0%
! TTGATGTTAGGTTTAAGATC+TGG - Chr2:80991013-80991032 MsG0280011210.01.T01:CDS 30.0%
!! AAATCTTCCATTTTGAGTAC+TGG - Chr2:80990767-80990786 MsG0280011210.01.T01:intron 30.0%
ACGAAGGTGATATGTTTGTT+AGG + Chr2:80990647-80990666 None:intergenic 35.0%
ATACAAAGTGAAGGCTAAAG+TGG - Chr2:80990873-80990892 MsG0280011210.01.T01:CDS 35.0%
CGGTAATAAGAAACCAGTAA+CGG - Chr2:80990963-80990982 MsG0280011210.01.T01:CDS 35.0%
CTCTCAAACAACATCAACAT+CGG - Chr2:80990692-80990711 MsG0280011210.01.T01:CDS 35.0%
GGAAAGTTTGAGAGATGTTA+CGG + Chr2:80990558-80990577 None:intergenic 35.0%
GGAATAAGAGTTACATGTGA+CGG - Chr2:80990919-80990938 MsG0280011210.01.T01:CDS 35.0%
GTAACTCTTATTCCAACGTT+AGG + Chr2:80990913-80990932 None:intergenic 35.0%
GTTGTTTGAGAGAATTGTGA+TGG + Chr2:80990684-80990703 None:intergenic 35.0%
TACAAAGTGAAGGCTAAAGT+GGG - Chr2:80990874-80990893 MsG0280011210.01.T01:CDS 35.0%
TGAAGTTGGATACAAAGTGA+AGG - Chr2:80990864-80990883 MsG0280011210.01.T01:CDS 35.0%
! CGAAGGTGATATGTTTGTTA+GGG + Chr2:80990646-80990665 None:intergenic 35.0%
! TTTAGCGTTGAAAGTGAAGT+TGG - Chr2:80990850-80990869 MsG0280011210.01.T01:CDS 35.0%
!!! GACGTTGAATTTTGAGTTGA+GGG + Chr2:80990606-80990625 None:intergenic 35.0%
!!! TGACGTTGAATTTTGAGTTG+AGG + Chr2:80990607-80990626 None:intergenic 35.0%
AACAACATCAACATCGGTGA+AGG - Chr2:80990698-80990717 MsG0280011210.01.T01:CDS 40.0%
ACCATACCAACTTTCACACA+TGG - Chr2:80990722-80990741 MsG0280011210.01.T01:CDS 40.0%
ATTAGAATCAGACGCTTCCA+CGG - Chr2:80990796-80990815 MsG0280011210.01.T01:CDS 40.0%
GTTAGAGTTCATGTTCCTGT+CGG - Chr2:80990943-80990962 MsG0280011210.01.T01:CDS 40.0%
GTTTGAGAGAATTGTGATGG+TGG + Chr2:80990681-80990700 None:intergenic 40.0%
TGCTTGACCAGTACTCAAAA+TGG + Chr2:80990777-80990796 None:intergenic 40.0%
TTCTTGCCATGTGTGAAAGT+TGG + Chr2:80990731-80990750 None:intergenic 40.0%
! AAAGGAGGATGAGAAGTATG+AGG + Chr2:80990475-80990494 None:intergenic 40.0%
! ACTGGTTTCTTATTACCGAC+AGG + Chr2:80990961-80990980 None:intergenic 40.0%
! CTTTTGTGGCTGGAAATGAT+GGG + Chr2:80990356-80990375 None:intergenic 40.0%
!!! GTTGAATTTTGAGTTGAGGG+TGG + Chr2:80990603-80990622 None:intergenic 40.0%
ACGGTAGATGAGGTAGAAAG+CGG + Chr2:80990517-80990536 None:intergenic 45.0%
GAGGAAGAACCAGAAGAAGA+AGG + Chr2:80990456-80990475 None:intergenic 45.0%
GCCACAAAAGCTCAACTCTA+CGG - Chr2:80990366-80990385 MsG0280011210.01.T01:CDS 45.0%
GTTTGAGAGATGTTACGGTG+AGG + Chr2:80990553-80990572 None:intergenic 45.0%
TTCTCATCCTCCTTTCTCCT+CGG - Chr2:80990480-80990499 MsG0280011210.01.T01:intron 45.0%
! ACCGTAGAGTTGAGCTTTTG+TGG + Chr2:80990370-80990389 None:intergenic 45.0%
! GCTTTTGTGGCTGGAAATGA+TGG + Chr2:80990357-80990376 None:intergenic 45.0%
! TAGAGTTGAGCTTTTGTGGC+TGG + Chr2:80990366-80990385 None:intergenic 45.0%
!! GAATTGTGATGGTGGTTGGT+TGG + Chr2:80990673-80990692 None:intergenic 45.0%
!! GAGAGAATTGTGATGGTGGT+TGG + Chr2:80990677-80990696 None:intergenic 45.0%
!! GCCATGTGTGAAAGTTGGTA+TGG + Chr2:80990726-80990745 None:intergenic 45.0%
!!! GAATTTTGAGTTGAGGGTGG+AGG + Chr2:80990600-80990619 None:intergenic 45.0%
CATGTTCTTCTTCAGCTCCG+TGG + Chr2:80990816-80990835 None:intergenic 50.0%
GAGAGATGTTACGGTGAGGA+AGG + Chr2:80990549-80990568 None:intergenic 50.0%
GATGTTACGGTGAGGAAGGA+CGG + Chr2:80990545-80990564 None:intergenic 50.0%
TTCGAAGTTGACGCCGTTAC+TGG + Chr2:80990979-80990998 None:intergenic 50.0%
! AGAAGAAGGTGCAGCAGCAA+CGG + Chr2:80990442-80990461 None:intergenic 50.0%
! GTCACCAACGGTAACGGTAA+CGG - Chr2:80990315-80990334 MsG0280011210.01.T01:CDS 50.0%
!! AACGGTGTCACCAACGGTAA+CGG - Chr2:80990309-80990328 MsG0280011210.01.T01:CDS 50.0%
!! GGCTGGAAATGATGGGTTTG+CGG + Chr2:80990349-80990368 None:intergenic 50.0%
!! GGTGGTTGGTTGGTAAACGA+AGG + Chr2:80990663-80990682 None:intergenic 50.0%
!! TGGAAATGATGGGTTTGCGG+CGG + Chr2:80990346-80990365 None:intergenic 50.0%
!!! TTTTGAGTTGAGGGTGGAGG+AGG + Chr2:80990597-80990616 None:intergenic 50.0%
CTCCTTTCTCCTCGGCGTAA+CGG - Chr2:80990488-80990507 MsG0280011210.01.T01:intron 55.0%
GACACCGTTACCGTTACCGT+TGG + Chr2:80990322-80990341 None:intergenic 55.0%
GAGGTTGTGGACGGTAGGTA+GGG + Chr2:80990401-80990420 None:intergenic 55.0%
GCTGCTGCACCTTCTTCTTC+TGG - Chr2:80990444-80990463 MsG0280011210.01.T01:CDS 55.0%
TCCTTTCTCCTCGGCGTAAC+GGG - Chr2:80990489-80990508 MsG0280011210.01.T01:intron 55.0%
TGAGGTTGTGGACGGTAGGT+AGG + Chr2:80990402-80990421 None:intergenic 55.0%
TTACGGTGAGGAAGGACGGT+GGG + Chr2:80990541-80990560 None:intergenic 55.0%
!! AACGGCAACGGTGTCACCAA+CGG - Chr2:80990303-80990322 MsG0280011210.01.T01:CDS 55.0%
CGTTACGCCGAGGAGAAAGG+AGG + Chr2:80990490-80990509 None:intergenic 60.0%
GGAGGAGGTGAGGTTGAGGT+AGG + Chr2:80990579-80990598 None:intergenic 60.0%
GTGGTGAGGTTGTGGACGGT+AGG + Chr2:80990406-80990425 None:intergenic 60.0%
GTTACGGTGAGGAAGGACGG+TGG + Chr2:80990542-80990561 None:intergenic 60.0%
GTTGTGGACGGTAGGTAGGG+CGG + Chr2:80990398-80990417 None:intergenic 60.0%
TACGGTGAGGAAGGACGGTG+GGG + Chr2:80990540-80990559 None:intergenic 60.0%
TGGAGGAGGAGGTGAGGTTG+AGG + Chr2:80990583-80990602 None:intergenic 60.0%
TTGTGGACGGTAGGTAGGGC+GGG + Chr2:80990397-80990416 None:intergenic 60.0%
! AGAAGGTGCAGCAGCAACGG+CGG + Chr2:80990439-80990458 None:intergenic 60.0%
! TGAGTTGAGGGTGGAGGAGG+AGG + Chr2:80990594-80990613 None:intergenic 60.0%
!! GTTGGTGACACCGTTGCCGT+TGG + Chr2:80990304-80990323 None:intergenic 60.0%
GACGGTGGGGACGGTAGATG+AGG + Chr2:80990527-80990546 None:intergenic 65.0%
GCCCGTTACGCCGAGGAGAA+AGG + Chr2:80990493-80990512 None:intergenic 65.0%
GGCGGTGGTGAGGTTGTGGA+CGG + Chr2:80990410-80990429 None:intergenic 65.0%
GTACGGCGGTGGTGAGGTTG+TGG + Chr2:80990414-80990433 None:intergenic 65.0%
GTGAGGAAGGACGGTGGGGA+CGG + Chr2:80990536-80990555 None:intergenic 65.0%
TGAGGGTGGAGGAGGAGGTG+AGG + Chr2:80990589-80990608 None:intergenic 65.0%
AAGCGGTGCCCGTTACGCCG+AGG + Chr2:80990500-80990519 None:intergenic 70.0%
AGGTGCAGCAGCAACGGCGG+CGG + Chr2:80990436-80990455 None:intergenic 70.0%
CAGCAGCAACGGCGGCGGTA+CGG + Chr2:80990431-80990450 None:intergenic 70.0%
TGGACGGTAGGTAGGGCGGG+TGG + Chr2:80990394-80990413 None:intergenic 70.0%
CAGCAACGGCGGCGGTACGG+CGG + Chr2:80990428-80990447 None:intergenic 75.0%
! CAACGGCGGCGGTACGGCGG+TGG + Chr2:80990425-80990444 None:intergenic 80.0%
! GCGGCGGTACGGCGGTGGTG+AGG + Chr2:80990420-80990439 None:intergenic 80.0%
Chromosome Type Strat End Strand Name
Chr2 gene 80990297 80991050 80990297 ID=MsG0280011210.01;Name=MsG0280011210.01
Chr2 mRNA 80990297 80991050 80990297 ID=MsG0280011210.01.T01;Parent=MsG0280011210.01;Name=MsG0280011210.01.T01;_AED=0.50;_eAED=0.50;_QI=0|0|0|1|0|0|3|0|228
Chr2 exon 80990297 80990483 80990297 ID=MsG0280011210.01.T01:exon:28795;Parent=MsG0280011210.01.T01
Chr2 exon 80990519 80990758 80990519 ID=MsG0280011210.01.T01:exon:28794;Parent=MsG0280011210.01.T01
Chr2 exon 80990791 80991050 80990791 ID=MsG0280011210.01.T01:exon:28793;Parent=MsG0280011210.01.T01
Chr2 CDS 80990791 80991050 80990791 ID=MsG0280011210.01.T01:cds;Parent=MsG0280011210.01.T01
Chr2 CDS 80990519 80990758 80990519 ID=MsG0280011210.01.T01:cds;Parent=MsG0280011210.01.T01
Chr2 CDS 80990297 80990483 80990297 ID=MsG0280011210.01.T01:cds;Parent=MsG0280011210.01.T01
Gene Sequence

>MsG0280011210.01.T01

ATGACCAACGGCAACGGTGTCACCAACGGTAACGGTAACGGTGTCTCCGCCGCAAACCCATCATTTCCAGCCACAAAAGCTCAACTCTACGGTGCCACCCGCCCTACCTACCGTCCACAACCTCACCACCGCCGTACCGCCGCCGTTGCTGCTGCACCTTCTTCTTCTGGTTCTTCCTCATACTTCTCATCCTCCTTTCTCCTCGGCGTAACGGGCACCGCTTTCTACCTCATCTACCGTCCCCACCGTCCTTCCTCACCCACCTCCTCCTCCACCCTCAACTCAAAATTCAACGTCAACATCACTGCAAAAAACCCTAACAAACATATCACCTTCGTTTACCAACCAACCACCATCACAATTCTCTCAAACAACATCAACATCGGTGAAGGAACCATACCAACTTTCACACATGGCAAGAAGAACACTACTCTTCTAAAATCTTCCATTTTGAGTACTGGTCAAGCATTAGAATCAGACGCTTCCACGGAGCTGAAGAATGAAGTTGGATACAAAGTGAAGGCTAAAGTGGGAAAAATGAAAACACCTAACGTTGGAATAAGAGTTACATGTGACGGTGTTAGAGTTCATGTTCCTGTCGGTAATAAGAAACCAGTAACGGCGTCAACTTCGAACGTTAAGTGTGATGTTGATGTTAGGTTTAAGATCTGGAAATGGACCGTTTAA
Protein sequence

>MsG0280011210.01.T01

MTNGNGVTNGNGNGVSAANPSFPATKAQLYGATRPTYRPQPHHRRTAAVAAAPSSSGSSSYFSSSFLLGVTGTAFYLIYRPHRPSSPTSSSTLNSKFNVNITAKNPNKHITFVYQPTTITILSNNINIGEGTIPTFTHGKKNTTLLKSSILSTGQALESDASTELKNEVGYKVKAKVGKMKTPNVGIRVTCDGVRVHVPVGNKKPVTASTSNVKCDVDVRFKIWKWTV*