AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene42805

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene42805.t1 MTR_8g011270 97.959 245 5 0 1 245 1 245 2.99e-176 504
MS.gene42805.t1 MTR_3g084740 55.102 245 104 2 7 245 8 252 2.17e-89 279
MS.gene42805.t1 MTR_3g084740 55.102 245 104 2 7 245 8 252 7.33e-89 279
MS.gene42805.t1 MTR_1g105605 35.827 254 130 6 4 245 2 234 2.88e-39 144
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene42805.t1 AT2G21630 60.569 246 93 3 3 245 2 246 1.71e-99 306
MS.gene42805.t1 AT3G23660 53.036 247 109 2 3 245 4 247 3.41e-88 277
MS.gene42805.t1 AT3G23660 53.036 247 109 2 3 245 4 247 5.87e-88 277
MS.gene42805.t1 AT1G05520 50.388 258 110 2 6 245 7 264 5.05e-84 266
MS.gene42805.t1 AT4G14160 51.639 244 116 2 4 245 11 254 8.17e-84 262
MS.gene42805.t1 AT4G14160 51.639 244 116 2 4 245 11 254 1.15e-82 263
MS.gene42805.t1 AT4G14160 51.639 244 116 2 4 245 11 254 1.28e-82 263
MS.gene42805.t1 AT5G43670 35.889 287 130 4 4 244 2 280 3.80e-54 186
MS.gene42805.t1 AT3G07100 23.204 181 119 6 14 175 321 500 3.41e-11 63.5

Find 76 sgRNAs with CRISPR-Local

Find 82 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTTGTTCATGTTCATGAATT+AGG 0.184876 8.2:-80660100 MS.gene42805:CDS
ACCTCTAAACACATAAGTTT+TGG 0.211068 8.2:+80660063 None:intergenic
TATGATTCCGTTAACGATTC+TGG 0.213494 8.2:-80660265 MS.gene42805:CDS
TTATGTGTTTAGAGGTAATA+AGG 0.254744 8.2:-80660056 MS.gene42805:CDS
CCCAAAACTTATGTGTTTAG+AGG 0.255169 8.2:-80660064 MS.gene42805:CDS
CTTGTTGGATTAATTACATT+TGG 0.277025 8.2:-80660127 MS.gene42805:CDS
CGGCAACGGAGAGGGGAGTA+TGG 0.291909 8.2:+80660451 None:intergenic
TTGTTCATGTTCATGAATTA+GGG 0.304124 8.2:-80660099 MS.gene42805:CDS
GAGATTGAAGCGTAATGATT+AGG 0.314527 8.2:+80660337 None:intergenic
CCGGCGGTTGGTGTTGTTGC+CGG 0.317183 8.2:-80659977 MS.gene42805:CDS
TCGATTTCGCCGCCAAGATC+TGG 0.350098 8.2:-80660393 MS.gene42805:CDS
TTGCCGGATAATTCGCTTGT+TGG 0.367608 8.2:-80660142 MS.gene42805:CDS
AGGTAATAAGGATTTGTCTA+AGG 0.373932 8.2:-80660044 MS.gene42805:CDS
CATGTTCATGAATTAGGGTT+TGG 0.387671 8.2:-80660094 MS.gene42805:CDS
TTGTTGGATTAATTACATTT+GGG 0.387705 8.2:-80660126 MS.gene42805:CDS
TGGCATTCGAACGCCGTCTT+GGG 0.406690 8.2:+80660576 None:intergenic
GTGTTTGATCGGAGTGTAGA+TGG 0.421489 8.2:+80660495 None:intergenic
ACAACACCAACCGCCGGCTT+CGG 0.425625 8.2:+80659983 None:intergenic
ATGGCATTCGAACGCCGTCT+TGG 0.425645 8.2:+80660575 None:intergenic
ACAGGCACATTACCGAGTTA+AGG 0.435855 8.2:+80659885 None:intergenic
TGTGTCATTGAGGAGGAGAT+TGG 0.449642 8.2:-80660202 MS.gene42805:CDS
TATGGGAGGAGTGGCATGGT+AGG 0.451947 8.2:+80660469 None:intergenic
CAGGCACATTACCGAGTTAA+GGG 0.452344 8.2:+80659886 None:intergenic
TATTCAACGGTTGTGTATTG+AGG 0.453130 8.2:+80660286 None:intergenic
AATGTGCCTGTCGGATAGTT+TGG 0.457774 8.2:-80659873 MS.gene42805:CDS
GTTGTTGCCGGTGCTCGTGA+TGG 0.459717 8.2:-80659965 MS.gene42805:CDS
AATCCAACAAGCGAATTATC+CGG 0.461492 8.2:+80660139 None:intergenic
TTTGTCTAAGGAGCAGTTGT+TGG 0.466913 8.2:-80660032 MS.gene42805:CDS
CGGAGTGTAGATGGCGGCGA+CGG 0.474002 8.2:+80660504 None:intergenic
ATGGGAGGAGTGGCATGGTA+GGG 0.477887 8.2:+80660470 None:intergenic
TTGTTGCCGGTGCTCGTGAT+GGG 0.489361 8.2:-80659964 MS.gene42805:CDS
CGAAAGCCCATCACGAGCAC+CGG 0.495627 8.2:+80659958 None:intergenic
AAACGGACAGATCCAGATCT+TGG 0.497672 8.2:+80660381 None:intergenic
GCGAATTCACATTCCGAAGA+AGG 0.501654 8.2:+80659908 None:intergenic
TTCTGGACCGCACGTGCCGC+CGG 0.501807 8.2:-80660248 MS.gene42805:CDS
GACAAGTGCGGCAACGGAGA+GGG 0.503799 8.2:+80660443 None:intergenic
GTGCCGGGGATTACGTTCCA+TGG 0.510397 8.2:+80660556 None:intergenic
GATTAGGAAAATGATTGCGT+TGG 0.511106 8.2:+80660353 None:intergenic
ATGTGAATTCGCCCTTAACT+CGG 0.523994 8.2:-80659897 MS.gene42805:CDS
GTGCGGTCCAGAATCGTTAA+CGG 0.524245 8.2:+80660258 None:intergenic
TTGAGCGACAAGTGCGGCAA+CGG 0.524314 8.2:+80660437 None:intergenic
GGAGTATGGGAGGAGTGGCA+TGG 0.531757 8.2:+80660465 None:intergenic
GACGGGAACGACGACGTTTG+TGG 0.534643 8.2:+80660522 None:intergenic
GGCAACGGAGAGGGGAGTAT+GGG 0.540332 8.2:+80660452 None:intergenic
GGAGTGTAGATGGCGGCGAC+GGG 0.540589 8.2:+80660505 None:intergenic
ACAAGTGCGGCAACGGAGAG+GGG 0.547069 8.2:+80660444 None:intergenic
CGACGATGCAGAAAGGATTG+AGG 0.547328 8.2:+80660413 None:intergenic
AAGAAACCGAAGCCGGCGGT+TGG 0.554678 8.2:-80659989 MS.gene42805:CDS
TTTCGCGAAGAAACCGAAGC+CGG 0.557841 8.2:-80659996 MS.gene42805:CDS
TGATTGCGTTGGAAGCAAAA+CGG 0.570935 8.2:+80660364 None:intergenic
AACGGAGAGGGGAGTATGGG+AGG 0.573093 8.2:+80660455 None:intergenic
CGCGAAGAAACCGAAGCCGG+CGG 0.573638 8.2:-80659993 MS.gene42805:CDS
TTTCGTCTGAGAGTATTTCG+AGG 0.576103 8.2:-80659940 MS.gene42805:CDS
AGAAACACCGGCGGCACGTG+CGG 0.580562 8.2:+80660241 None:intergenic
ACACAGCCAAACTATCCGAC+AGG 0.580811 8.2:+80659867 None:intergenic
AATCTCTGAAGATAATATGC+CGG 0.582915 8.2:-80660320 MS.gene42805:CDS
GCGAAATCGACGATGCAGAA+AGG 0.585468 8.2:+80660406 None:intergenic
AGAGGGGAGTATGGGAGGAG+TGG 0.589081 8.2:+80660460 None:intergenic
ATGGTAGGGAAGTGTTTGAT+CGG 0.591783 8.2:+80660484 None:intergenic
CTCAACAGCTTGAGAAATCG+CGG 0.598170 8.2:+80660168 None:intergenic
TGTTGACACGTGTGTCATTG+AGG 0.600014 8.2:-80660212 MS.gene42805:CDS
ATCGATCTCGAAACCCAAGA+CGG 0.614827 8.2:-80660589 MS.gene42805:CDS
AAGACGGCGTTCGAATGCCA+TGG 0.617736 8.2:-80660573 MS.gene42805:CDS
TCCTTTCATCAATATGACGA+CGG 0.619333 8.2:-80660617 None:intergenic
CCGGCAACAACACCAACCGC+CGG 0.620192 8.2:+80659977 None:intergenic
GTTAACGGAATCATATTCAA+CGG 0.624484 8.2:+80660273 None:intergenic
CGACAAGTGCGGCAACGGAG+AGG 0.626785 8.2:+80660442 None:intergenic
CGGACAGATCCAGATCTTGG+CGG 0.627606 8.2:+80660384 None:intergenic
ATGCCATGGAACGTAATCCC+CGG 0.637422 8.2:-80660559 MS.gene42805:CDS
TCAACAACAAACAGAAACAC+CGG 0.658553 8.2:+80660229 None:intergenic
TAACTCGGTAATGTGCCTGT+CGG 0.664279 8.2:-80659882 MS.gene42805:CDS
CTCTGAAGATAATATGCCGG+CGG 0.666214 8.2:-80660317 MS.gene42805:CDS
TGAGGATTGAGCGACAAGTG+CGG 0.675483 8.2:+80660431 None:intergenic
ACAACAAACAGAAACACCGG+CGG 0.717071 8.2:+80660232 None:intergenic
TGACACGTGTGTCATTGAGG+AGG 0.750317 8.2:-80660209 MS.gene42805:CDS
TTTGATCGGAGTGTAGATGG+CGG 0.766423 8.2:+80660498 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TTGTTGGATTAATTACATTT+GGG - chr8.2:80660340-80660359 MS.gene42805:CDS 20.0%
! CTTGTTGGATTAATTACATT+TGG - chr8.2:80660339-80660358 MS.gene42805:CDS 25.0%
! TTATGTGTTTAGAGGTAATA+AGG - chr8.2:80660410-80660429 MS.gene42805:CDS 25.0%
! TTGTTCATGTTCATGAATTA+GGG - chr8.2:80660367-80660386 MS.gene42805:CDS 25.0%
! TTTGTTCATGTTCATGAATT+AGG - chr8.2:80660366-80660385 MS.gene42805:CDS 25.0%
AGGTAATAAGGATTTGTCTA+AGG - chr8.2:80660422-80660441 MS.gene42805:CDS 30.0%
GTTAACGGAATCATATTCAA+CGG + chr8.2:80660196-80660215 None:intergenic 30.0%
! AATCTCTGAAGATAATATGC+CGG - chr8.2:80660146-80660165 MS.gene42805:CDS 30.0%
! ACCTCTAAACACATAAGTTT+TGG + chr8.2:80660406-80660425 None:intergenic 30.0%
! CCTCTAAACACATAAGTTTT+GGG + chr8.2:80660405-80660424 None:intergenic 30.0%
AATCCAACAAGCGAATTATC+CGG + chr8.2:80660330-80660349 None:intergenic 35.0%
CATGTTCATGAATTAGGGTT+TGG - chr8.2:80660372-80660391 MS.gene42805:CDS 35.0%
CCCAAAACTTATGTGTTTAG+AGG - chr8.2:80660402-80660421 MS.gene42805:CDS 35.0%
GAGATTGAAGCGTAATGATT+AGG + chr8.2:80660132-80660151 None:intergenic 35.0%
GATTAGGAAAATGATTGCGT+TGG + chr8.2:80660116-80660135 None:intergenic 35.0%
TATGATTCCGTTAACGATTC+TGG - chr8.2:80660201-80660220 MS.gene42805:CDS 35.0%
TATTCAACGGTTGTGTATTG+AGG + chr8.2:80660183-80660202 None:intergenic 35.0%
TCAACAACAAACAGAAACAC+CGG + chr8.2:80660240-80660259 None:intergenic 35.0%
ATGTGAATTCGCCCTTAACT+CGG - chr8.2:80660569-80660588 MS.gene42805:CDS 40.0%
TGATTGCGTTGGAAGCAAAA+CGG + chr8.2:80660105-80660124 None:intergenic 40.0%
TTTGTCTAAGGAGCAGTTGT+TGG - chr8.2:80660434-80660453 MS.gene42805:CDS 40.0%
! GAGGTTTTTGCTTCCTTCTT+CGG - chr8.2:80660545-80660564 MS.gene42805:CDS 40.0%
!! ATGGTAGGGAAGTGTTTGAT+CGG + chr8.2:80659985-80660004 None:intergenic 40.0%
!! TTTCGTCTGAGAGTATTTCG+AGG - chr8.2:80660526-80660545 MS.gene42805:CDS 40.0%
!!! TGTGGATTCTTGTTTTGTGC+CGG + chr8.2:80659929-80659948 None:intergenic 40.0%
AAACGGACAGATCCAGATCT+TGG + chr8.2:80660088-80660107 None:intergenic 45.0%
AATGTGCCTGTCGGATAGTT+TGG - chr8.2:80660593-80660612 MS.gene42805:CDS 45.0%
ACAACAAACAGAAACACCGG+CGG + chr8.2:80660237-80660256 None:intergenic 45.0%
ACAGGCACATTACCGAGTTA+AGG + chr8.2:80660584-80660603 None:intergenic 45.0%
ATCGATCTCGAAACCCAAGA+CGG - chr8.2:80659877-80659896 MS.gene42805:CDS 45.0%
CAGGCACATTACCGAGTTAA+GGG + chr8.2:80660583-80660602 None:intergenic 45.0%
CTCAACAGCTTGAGAAATCG+CGG + chr8.2:80660301-80660320 None:intergenic 45.0%
GCGAATTCACATTCCGAAGA+AGG + chr8.2:80660561-80660580 None:intergenic 45.0%
GTGTTTGATCGGAGTGTAGA+TGG + chr8.2:80659974-80659993 None:intergenic 45.0%
TAACTCGGTAATGTGCCTGT+CGG - chr8.2:80660584-80660603 MS.gene42805:CDS 45.0%
TATTGAGGAAAAAGCTCCGC+CGG + chr8.2:80660168-80660187 None:intergenic 45.0%
TTGCCGGATAATTCGCTTGT+TGG - chr8.2:80660324-80660343 MS.gene42805:CDS 45.0%
TTTGATCGGAGTGTAGATGG+CGG + chr8.2:80659971-80659990 None:intergenic 45.0%
! CTCTGAAGATAATATGCCGG+CGG - chr8.2:80660149-80660168 MS.gene42805:CDS 45.0%
! TCAAGCTGTTGAGCTTTTGC+CGG - chr8.2:80660308-80660327 MS.gene42805:CDS 45.0%
! TGTGTCATTGAGGAGGAGAT+TGG - chr8.2:80660264-80660283 MS.gene42805:CDS 45.0%
! TGTTGACACGTGTGTCATTG+AGG - chr8.2:80660254-80660273 MS.gene42805:CDS 45.0%
!!! GTGGATTCTTGTTTTGTGCC+GGG + chr8.2:80659928-80659947 None:intergenic 45.0%
!!! TGGATTCTTGTTTTGTGCCG+GGG + chr8.2:80659927-80659946 None:intergenic 45.0%
ACACAGCCAAACTATCCGAC+AGG + chr8.2:80660602-80660621 None:intergenic 50.0%
ATGCCATGGAACGTAATCCC+CGG - chr8.2:80659907-80659926 MS.gene42805:CDS 50.0%
CGACGATGCAGAAAGGATTG+AGG + chr8.2:80660056-80660075 None:intergenic 50.0%
GCGAAATCGACGATGCAGAA+AGG + chr8.2:80660063-80660082 None:intergenic 50.0%
GTGCGGTCCAGAATCGTTAA+CGG + chr8.2:80660211-80660230 None:intergenic 50.0%
TGAGGATTGAGCGACAAGTG+CGG + chr8.2:80660038-80660057 None:intergenic 50.0%
TTTCGCGAAGAAACCGAAGC+CGG - chr8.2:80660470-80660489 MS.gene42805:CDS 50.0%
! TGACACGTGTGTCATTGAGG+AGG - chr8.2:80660257-80660276 MS.gene42805:CDS 50.0%
AAGACGGCGTTCGAATGCCA+TGG - chr8.2:80659893-80659912 MS.gene42805:CDS 55.0%
ATGGCATTCGAACGCCGTCT+TGG + chr8.2:80659894-80659913 None:intergenic 55.0%
ATGGGAGGAGTGGCATGGTA+GGG + chr8.2:80659999-80660018 None:intergenic 55.0%
CGGACAGATCCAGATCTTGG+CGG + chr8.2:80660085-80660104 None:intergenic 55.0%
TATGGGAGGAGTGGCATGGT+AGG + chr8.2:80660000-80660019 None:intergenic 55.0%
TCGATTTCGCCGCCAAGATC+TGG - chr8.2:80660073-80660092 MS.gene42805:CDS 55.0%
TGGCATTCGAACGCCGTCTT+GGG + chr8.2:80659893-80659912 None:intergenic 55.0%
TTGAGCGACAAGTGCGGCAA+CGG + chr8.2:80660032-80660051 None:intergenic 55.0%
TTGTTGCCGGTGCTCGTGAT+GGG - chr8.2:80660502-80660521 MS.gene42805:CDS 55.0%
AAGAAACCGAAGCCGGCGGT+TGG - chr8.2:80660477-80660496 MS.gene42805:CDS 60.0%
ACAAGTGCGGCAACGGAGAG+GGG + chr8.2:80660025-80660044 None:intergenic 60.0%
CGAAAGCCCATCACGAGCAC+CGG + chr8.2:80660511-80660530 None:intergenic 60.0%
GACAAGTGCGGCAACGGAGA+GGG + chr8.2:80660026-80660045 None:intergenic 60.0%
GACGGGAACGACGACGTTTG+TGG + chr8.2:80659947-80659966 None:intergenic 60.0%
GGAGTATGGGAGGAGTGGCA+TGG + chr8.2:80660004-80660023 None:intergenic 60.0%
GTGCCGGGGATTACGTTCCA+TGG + chr8.2:80659913-80659932 None:intergenic 60.0%
GTTGTTGCCGGTGCTCGTGA+TGG - chr8.2:80660501-80660520 MS.gene42805:CDS 60.0%
! AACGGAGAGGGGAGTATGGG+AGG + chr8.2:80660014-80660033 None:intergenic 60.0%
! AGAGGGGAGTATGGGAGGAG+TGG + chr8.2:80660009-80660028 None:intergenic 60.0%
! GGCAACGGAGAGGGGAGTAT+GGG + chr8.2:80660017-80660036 None:intergenic 60.0%
!! ACAACACCAACCGCCGGCTT+CGG + chr8.2:80660486-80660505 None:intergenic 60.0%
AGAAACACCGGCGGCACGTG+CGG + chr8.2:80660228-80660247 None:intergenic 65.0%
CCGGCAACAACACCAACCGC+CGG + chr8.2:80660492-80660511 None:intergenic 65.0%
CGACAAGTGCGGCAACGGAG+AGG + chr8.2:80660027-80660046 None:intergenic 65.0%
CGCGAAGAAACCGAAGCCGG+CGG - chr8.2:80660473-80660492 MS.gene42805:CDS 65.0%
CGGCAACGGAGAGGGGAGTA+TGG + chr8.2:80660018-80660037 None:intergenic 65.0%
! CGGAGTGTAGATGGCGGCGA+CGG + chr8.2:80659965-80659984 None:intergenic 65.0%
! GGAGTGTAGATGGCGGCGAC+GGG + chr8.2:80659964-80659983 None:intergenic 65.0%
!! CCGGCGGTTGGTGTTGTTGC+CGG - chr8.2:80660489-80660508 MS.gene42805:CDS 65.0%
TTCTGGACCGCACGTGCCGC+CGG - chr8.2:80660218-80660237 MS.gene42805:CDS 70.0%


Chromosome Type Strat End Strand Name
chr8.2 gene 80659862 80660626 80659862 ID=MS.gene42805
chr8.2 mRNA 80659862 80660626 80659862 ID=MS.gene42805.t1;Parent=MS.gene42805
chr8.2 exon 80659862 80660626 80659862 ID=MS.gene42805.t1.exon1;Parent=MS.gene42805.t1
chr8.2 CDS 80659862 80660626 80659862 ID=cds.MS.gene42805.t1;Parent=MS.gene42805.t1
Gene Sequence

>MS.gene42805

ATGACGACGGAATTCATCGATCTCGAAACCCAAGACGGCGTTCGAATGCCATGGAACGTAATCCCCGGCACAAAACAAGAATCCACAAACGTCGTCGTTCCCGTCGCCGCCATCTACACTCCGATCAAACACTTCCCTACCATGCCACTCCTCCCATACTCCCCTCTCCGTTGCCGCACTTGTCGCTCAATCCTCAATCCTTTCTGCATCGTCGATTTCGCCGCCAAGATCTGGATCTGTCCGTTTTGCTTCCAACGCAATCATTTTCCTAATCATTACGCTTCAATCTCTGAAGATAATATGCCGGCGGAGCTTTTTCCTCAATACACAACCGTTGAATATGATTCCGTTAACGATTCTGGACCGCACGTGCCGCCGGTGTTTCTGTTTGTTGTTGACACGTGTGTCATTGAGGAGGAGATTGGTTTTCTTCGATCCGCGATTTCTCAAGCTGTTGAGCTTTTGCCGGATAATTCGCTTGTTGGATTAATTACATTTGGGAGTTTTGTTCATGTTCATGAATTAGGGTTTGGTATTGTTCCCAAAACTTATGTGTTTAGAGGTAATAAGGATTTGTCTAAGGAGCAGTTGTTGGAGCAGATGAATTTTTTCGCGAAGAAACCGAAGCCGGCGGTTGGTGTTGTTGCCGGTGCTCGTGATGGGCTTTCGTCTGAGAGTATTTCGAGGTTTTTGCTTCCTTCTTCGGAATGTGAATTCGCCCTTAACTCGGTAATGTGCCTGTCGGATAGTTTGGCTGTGTGTTGA
Protein sequence

>MS.gene42805.t1

MTTEFIDLETQDGVRMPWNVIPGTKQESTNVVVPVAAIYTPIKHFPTMPLLPYSPLRCRTCRSILNPFCIVDFAAKIWICPFCFQRNHFPNHYASISEDNMPAELFPQYTTVEYDSVNDSGPHVPPVFLFVVDTCVIEEEIGFLRSAISQAVELLPDNSLVGLITFGSFVHVHELGFGIVPKTYVFRGNKDLSKEQLLEQMNFFAKKPKPAVGVVAGARDGLSSESISRFLLPSSECEFALNSVMCLSDSLAVC