AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene020102

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene020102.t1 MTR_8g012210 95.601 341 15 0 2 342 30 370 0.0 677
MS.gene020102.t1 MTR_2g437260 20.130 308 233 9 35 335 80 381 5.11e-12 66.6
MS.gene020102.t1 MTR_4g120380 21.498 307 226 8 19 319 72 369 5.70e-12 66.6
MS.gene020102.t1 MTR_2g436460 21.212 297 218 9 30 319 86 373 1.54e-11 65.1
MS.gene020102.t1 MTR_6g083110 56.364 55 20 1 244 298 1 51 2.31e-11 62.0
MS.gene020102.t1 MTR_4g120380 20.521 307 230 7 19 319 72 370 2.86e-11 64.7
MS.gene020102.t1 MTR_2g019810 22.727 308 170 11 30 323 107 360 8.75e-11 62.8
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene020102.t1 AT1G79220 48.485 330 165 3 16 342 72 399 1.16e-105 315
MS.gene020102.t1 AT1G21150 22.047 254 194 4 20 269 47 300 4.02e-11 63.9
MS.gene020102.t1 AT1G21150 22.047 254 194 4 20 269 83 336 4.19e-11 63.9
MS.gene020102.t1 AT1G21150 22.047 254 194 4 20 269 147 400 6.35e-11 63.5

Find 58 sgRNAs with CRISPR-Local

Find 80 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ACTTCGCTTGCTTAGTGATT+TGG 0.257285 8.3:+77051549 MS.gene020102:CDS
GTTGACAATGTCAAAATATT+AGG 0.276459 8.3:-77052030 None:intergenic
CTTCGCTTGCTTAGTGATTT+GGG 0.280618 8.3:+77051550 MS.gene020102:CDS
GGAAATTGCTGATGAGTTAA+TGG 0.297355 8.3:+77052290 MS.gene020102:CDS
TTGCTTAGTGATTTGGGTTT+AGG 0.299185 8.3:+77051556 MS.gene020102:CDS
AAATATGTGGTGACATTAAT+AGG 0.301744 8.3:+77051913 MS.gene020102:CDS
TAGCAGTTTCATCAAGGAAT+TGG 0.311012 8.3:+77052346 MS.gene020102:CDS
CAAGCCTCTCGTCGAAATTA+TGG 0.312035 8.3:-77051639 None:intergenic
AGCAATGAAGGTACAGAATA+TGG 0.327499 8.3:+77052179 MS.gene020102:CDS
GTTAAACAATATGAAGAGTT+AGG 0.347136 8.3:+77051763 MS.gene020102:CDS
ATATTTGAAAACAACAGATA+TGG 0.357754 8.3:-77052126 None:intergenic
TTTGACATTGTCAACTGATA+AGG 0.368653 8.3:+77052038 MS.gene020102:CDS
TGCAAAATGTTGAAGACAAA+TGG 0.380077 8.3:+77051413 MS.gene020102:CDS
TTCATTGCTAGAAGCACTCT+TGG 0.407140 8.3:-77052165 None:intergenic
GCGCAATGCGGATCCTTCTC+AGG 0.407457 8.3:+77051516 MS.gene020102:CDS
TATGTCATTGTTTGAGTCAA+AGG 0.408420 8.3:+77051669 MS.gene020102:CDS
TTGTAAAGATTATCAATTGT+AGG 0.408436 8.3:+77051590 MS.gene020102:CDS
CATCAGCAATTTCCTTATCA+TGG 0.411377 8.3:-77052281 None:intergenic
TTGTCGGATGATGAGATATT+CGG 0.417333 8.3:+77051991 MS.gene020102:CDS
CGTGGAAACAATTCGCGAAA+AGG 0.422845 8.3:+77051945 MS.gene020102:CDS
AGCTGGGACTTTCGTCGAAT+AGG 0.432888 8.3:-77051374 None:intergenic
CCTCAATGCTCTAAGTATTG+AGG 0.451275 8.3:-77052220 None:intergenic
CTCAATGCTCTAAGTATTGA+GGG 0.456627 8.3:-77052219 None:intergenic
TTCCTTTGACGATGAGAAGA+TGG 0.459653 8.3:+77051846 MS.gene020102:CDS
ATGGAATATATAAGTAGGAC+TGG 0.464288 8.3:+77051865 MS.gene020102:CDS
AAGAGTTAGGTATACCGAAA+AGG 0.464523 8.3:+77051776 MS.gene020102:CDS
GTCAAAGGAAATGCTTCATA+AGG 0.473131 8.3:+77051684 MS.gene020102:CDS
GATCCGCATTGCGCAAAGAC+GGG 0.492040 8.3:-77051507 None:intergenic
GGGTTGTGGTGATGACGATT+TGG 0.493364 8.3:+77051465 MS.gene020102:CDS
ATATAAAAGTAGTTCAGAAA+GGG 0.499107 8.3:-77052383 None:intergenic
AGAGTTAGGTATACCGAAAA+GGG 0.502937 8.3:+77051777 MS.gene020102:CDS
TTCAAAATTGTACAAATATG+TGG 0.504006 8.3:+77051900 MS.gene020102:CDS
GTTTGTCAGATGCCATGATA+AGG 0.508257 8.3:+77052269 MS.gene020102:CDS
AGGTATACCGAAAAGGGACT+TGG 0.508376 8.3:+77051783 MS.gene020102:CDS
TATTTGAAAACAACAGATAT+GGG 0.512551 8.3:-77052125 None:intergenic
AATATAAAAGTAGTTCAGAA+AGG 0.519070 8.3:-77052384 None:intergenic
GGATCCGCATTGCGCAAAGA+CGG 0.525836 8.3:-77051508 None:intergenic
AGAGATTAGCAGTTTCATCA+AGG 0.527319 8.3:+77052340 MS.gene020102:CDS
AAGAGTGCTTCTAGCAATGA+AGG 0.527541 8.3:+77052167 MS.gene020102:CDS
CAATGAAGGGTTTCTTGCAA+TGG 0.534493 8.3:-77051707 None:intergenic
AGAAGATGGAATATATAAGT+AGG 0.535407 8.3:+77051860 MS.gene020102:CDS
TTCCATCTTCTCATCGTCAA+AGG 0.562047 8.3:-77051848 None:intergenic
AAGTAGGACTGGGCTTTCCA+AGG 0.567180 8.3:+77051876 MS.gene020102:CDS
TCAAGGAATTGGACTACTAG+AGG 0.573509 8.3:+77052357 MS.gene020102:CDS
CATTGAGGATGTCCGAGGAG+AGG 0.582695 8.3:+77052235 MS.gene020102:CDS
ACTTTCGTCGAATAGGTGGC+AGG 0.582772 8.3:-77051367 None:intergenic
ATTAATAGGCATCTCTCGCG+TGG 0.592649 8.3:+77051927 MS.gene020102:CDS
TGTCAACTGATAAGGTTCAA+AGG 0.601835 8.3:+77052046 MS.gene020102:CDS
GAAAGTCCCAGCTCAAAATG+AGG 0.604863 8.3:+77051384 MS.gene020102:CDS
CCTCAATACTTAGAGCATTG+AGG 0.607754 8.3:+77052220 MS.gene020102:CDS
TGGAATATATAAGTAGGACT+GGG 0.608434 8.3:+77051866 MS.gene020102:CDS
TGGGACTTTCGTCGAATAGG+TGG 0.610226 8.3:-77051371 None:intergenic
TTAACCATAATTTCGACGAG+AGG 0.625796 8.3:+77051635 MS.gene020102:CDS
AGTTTCGACTGAACCTGAGA+AGG 0.646506 8.3:-77051529 None:intergenic
AAATGTTGAAGACAAATGGA+AGG 0.655802 8.3:+77051417 MS.gene020102:CDS
GAAGTTCTTGAAATAACCGT+CGG 0.665623 8.3:-77051826 None:intergenic
TAGAGCATTGAGGATGTCCG+AGG 0.681763 8.3:+77052230 MS.gene020102:CDS
TTGCCCGTCTTTGCGCAATG+CGG 0.689638 8.3:+77051504 MS.gene020102:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! AGTTAATGGAATTTTATAAA+AGG + chr8.3:77052304-77052323 MS.gene020102:CDS 15.0%
!! ATATTTGAAAACAACAGATA+TGG - chr8.3:77052129-77052148 None:intergenic 20.0%
!! TATTTGAAAACAACAGATAT+GGG - chr8.3:77052128-77052147 None:intergenic 20.0%
!! TTCAAAATTGTACAAATATG+TGG + chr8.3:77051900-77051919 MS.gene020102:CDS 20.0%
!! TTGTAAAGATTATCAATTGT+AGG + chr8.3:77051590-77051609 MS.gene020102:CDS 20.0%
!!! ATATCTGTTGTTTTCAAATA+TGG + chr8.3:77052128-77052147 MS.gene020102:CDS 20.0%
!!! ATTTTATAAAAGGACAAAAC+AGG + chr8.3:77052314-77052333 MS.gene020102:CDS 20.0%
! AAATATGTGGTGACATTAAT+AGG + chr8.3:77051913-77051932 MS.gene020102:CDS 25.0%
! AGAAGATGGAATATATAAGT+AGG + chr8.3:77051860-77051879 MS.gene020102:CDS 25.0%
! GTTAAACAATATGAAGAGTT+AGG + chr8.3:77051763-77051782 MS.gene020102:CDS 25.0%
! GTTGACAATGTCAAAATATT+AGG - chr8.3:77052033-77052052 None:intergenic 25.0%
!! GTGTTGAATTTTACAAAGTA+TGG + chr8.3:77051967-77051986 MS.gene020102:CDS 25.0%
!! TTTGTACAATTTTGAATCCT+TGG - chr8.3:77051896-77051915 None:intergenic 25.0%
!!! TACTGAAGTTTTGAGTAAAT+GGG + chr8.3:77051444-77051463 MS.gene020102:CDS 25.0%
!!! TTTTACAAAGTATGGTTTGT+CGG + chr8.3:77051975-77051994 MS.gene020102:CDS 25.0%
AAATGTTGAAGACAAATGGA+AGG + chr8.3:77051417-77051436 MS.gene020102:CDS 30.0%
ATGGAATATATAAGTAGGAC+TGG + chr8.3:77051865-77051884 MS.gene020102:CDS 30.0%
TATGTCATTGTTTGAGTCAA+AGG + chr8.3:77051669-77051688 MS.gene020102:CDS 30.0%
TGCAAAATGTTGAAGACAAA+TGG + chr8.3:77051413-77051432 MS.gene020102:CDS 30.0%
TGGAATATATAAGTAGGACT+GGG + chr8.3:77051866-77051885 MS.gene020102:CDS 30.0%
TTTGACATTGTCAACTGATA+AGG + chr8.3:77052038-77052057 MS.gene020102:CDS 30.0%
! AGGAACATGACTTTCATTTT+AGG + chr8.3:77052066-77052085 MS.gene020102:CDS 30.0%
! ATGAGATATTCGGTCTTTTT+GGG + chr8.3:77052001-77052020 MS.gene020102:CDS 30.0%
! TATTTTCACACAGCAATGAA+GGG - chr8.3:77051723-77051742 None:intergenic 30.0%
! TGGTTCAAATGATGATTTTG+CGG + chr8.3:77051803-77051822 MS.gene020102:CDS 30.0%
! TTATTTTCACACAGCAATGA+AGG - chr8.3:77051724-77051743 None:intergenic 30.0%
!!! ACTGAAGTTTTGAGTAAATG+GGG + chr8.3:77051445-77051464 MS.gene020102:CDS 30.0%
!!! ATTGAGGGTGTTTTCATATT+AGG - chr8.3:77052207-77052226 None:intergenic 30.0%
!!! CTACTGAAGTTTTGAGTAAA+TGG + chr8.3:77051443-77051462 MS.gene020102:CDS 30.0%
AAGAGTTAGGTATACCGAAA+AGG + chr8.3:77051776-77051795 MS.gene020102:CDS 35.0%
AGAGATTAGCAGTTTCATCA+AGG + chr8.3:77052340-77052359 MS.gene020102:CDS 35.0%
AGAGTTAGGTATACCGAAAA+GGG + chr8.3:77051777-77051796 MS.gene020102:CDS 35.0%
CATCAGCAATTTCCTTATCA+TGG - chr8.3:77052284-77052303 None:intergenic 35.0%
GAAGTTCTTGAAATAACCGT+CGG - chr8.3:77051829-77051848 None:intergenic 35.0%
GGAAATTGCTGATGAGTTAA+TGG + chr8.3:77052290-77052309 MS.gene020102:CDS 35.0%
GTCAAAGGAAATGCTTCATA+AGG + chr8.3:77051684-77051703 MS.gene020102:CDS 35.0%
TAGCAGTTTCATCAAGGAAT+TGG + chr8.3:77052346-77052365 MS.gene020102:CDS 35.0%
TGTCAACTGATAAGGTTCAA+AGG + chr8.3:77052046-77052065 MS.gene020102:CDS 35.0%
TTAACCATAATTTCGACGAG+AGG + chr8.3:77051635-77051654 MS.gene020102:CDS 35.0%
TTGTCGGATGATGAGATATT+CGG + chr8.3:77051991-77052010 MS.gene020102:CDS 35.0%
! AGCAATGAAGGTACAGAATA+TGG + chr8.3:77052179-77052198 MS.gene020102:CDS 35.0%
! ATTTCAACCTCATTTTGAGC+TGG - chr8.3:77051394-77051413 None:intergenic 35.0%
! ATTTGAACCAAGTCCCTTTT+CGG - chr8.3:77051793-77051812 None:intergenic 35.0%
! GATGAGATATTCGGTCTTTT+TGG + chr8.3:77052000-77052019 MS.gene020102:CDS 35.0%
! TTGCTTAGTGATTTGGGTTT+AGG + chr8.3:77051556-77051575 MS.gene020102:CDS 35.0%
! TTTCAACCTCATTTTGAGCT+GGG - chr8.3:77051393-77051412 None:intergenic 35.0%
!! CTCAATGCTCTAAGTATTGA+GGG - chr8.3:77052222-77052241 None:intergenic 35.0%
ACTTCGCTTGCTTAGTGATT+TGG + chr8.3:77051549-77051568 MS.gene020102:CDS 40.0%
CAATGAAGGGTTTCTTGCAA+TGG - chr8.3:77051710-77051729 None:intergenic 40.0%
CGTATTGAAAAACCTCTCCT+CGG - chr8.3:77052250-77052269 None:intergenic 40.0%
CTTCGCTTGCTTAGTGATTT+GGG + chr8.3:77051550-77051569 MS.gene020102:CDS 40.0%
GTTTGTCAGATGCCATGATA+AGG + chr8.3:77052269-77052288 MS.gene020102:CDS 40.0%
TCAAGGAATTGGACTACTAG+AGG + chr8.3:77052357-77052376 MS.gene020102:CDS 40.0%
TTCCATCTTCTCATCGTCAA+AGG - chr8.3:77051851-77051870 None:intergenic 40.0%
TTCCTTTGACGATGAGAAGA+TGG + chr8.3:77051846-77051865 MS.gene020102:CDS 40.0%
! ATTGTAGGCCTCGATTTTTC+AGG + chr8.3:77051605-77051624 MS.gene020102:CDS 40.0%
! CCTCAATGCTCTAAGTATTG+AGG - chr8.3:77052223-77052242 None:intergenic 40.0%
!! AAGAGTGCTTCTAGCAATGA+AGG + chr8.3:77052167-77052186 MS.gene020102:CDS 40.0%
!! CCTCAATACTTAGAGCATTG+AGG + chr8.3:77052220-77052239 MS.gene020102:CDS 40.0%
!! GTTTTGAGTAAATGGGGTTG+TGG + chr8.3:77051451-77051470 MS.gene020102:CDS 40.0%
!! TTCATTGCTAGAAGCACTCT+TGG - chr8.3:77052168-77052187 None:intergenic 40.0%
AGGTATACCGAAAAGGGACT+TGG + chr8.3:77051783-77051802 MS.gene020102:CDS 45.0%
AGTCGAGTCCTGAAAAATCG+AGG - chr8.3:77051616-77051635 None:intergenic 45.0%
AGTTTCGACTGAACCTGAGA+AGG - chr8.3:77051532-77051551 None:intergenic 45.0%
ATTAATAGGCATCTCTCGCG+TGG + chr8.3:77051927-77051946 MS.gene020102:CDS 45.0%
CAAGCCTCTCGTCGAAATTA+TGG - chr8.3:77051642-77051661 None:intergenic 45.0%
CGTGGAAACAATTCGCGAAA+AGG + chr8.3:77051945-77051964 MS.gene020102:CDS 45.0%
GAAAGTCCCAGCTCAAAATG+AGG + chr8.3:77051384-77051403 MS.gene020102:CDS 45.0%
! AATGATGATTTTGCGGCCGA+CGG + chr8.3:77051810-77051829 MS.gene020102:CDS 45.0%
AAGTAGGACTGGGCTTTCCA+AGG + chr8.3:77051876-77051895 MS.gene020102:CDS 50.0%
ACTTTCGTCGAATAGGTGGC+AGG - chr8.3:77051370-77051389 None:intergenic 50.0%
AGCTGGGACTTTCGTCGAAT+AGG - chr8.3:77051377-77051396 None:intergenic 50.0%
TGGGACTTTCGTCGAATAGG+TGG - chr8.3:77051374-77051393 None:intergenic 50.0%
! GGGTTGTGGTGATGACGATT+TGG + chr8.3:77051465-77051484 MS.gene020102:CDS 50.0%
!! TAGAGCATTGAGGATGTCCG+AGG + chr8.3:77052230-77052249 MS.gene020102:CDS 50.0%
CATTGAGGATGTCCGAGGAG+AGG + chr8.3:77052235-77052254 MS.gene020102:CDS 55.0%
GATCCGCATTGCGCAAAGAC+GGG - chr8.3:77051510-77051529 None:intergenic 55.0%
GGATCCGCATTGCGCAAAGA+CGG - chr8.3:77051511-77051530 None:intergenic 55.0%
TTGCCCGTCTTTGCGCAATG+CGG + chr8.3:77051504-77051523 MS.gene020102:CDS 55.0%
GCGCAATGCGGATCCTTCTC+AGG + chr8.3:77051516-77051535 MS.gene020102:CDS 60.0%


Chromosome Type Strat End Strand Name
chr8.3 gene 77051364 77052392 77051364 ID=MS.gene020102
chr8.3 mRNA 77051364 77052392 77051364 ID=MS.gene020102.t1;Parent=MS.gene020102
chr8.3 exon 77051364 77052392 77051364 ID=MS.gene020102.t1.exon1;Parent=MS.gene020102.t1
chr8.3 CDS 77051364 77052392 77051364 ID=cds.MS.gene020102.t1;Parent=MS.gene020102.t1
Gene Sequence

>MS.gene020102

ATGCCTGCCACCTATTCGACGAAAGTCCCAGCTCAAAATGAGGTTGAAATGCAAAATGTTGAAGACAAATGGAAGGATGCTACTGAAGTTTTGAGTAAATGGGGTTGTGGTGATGACGATTTGGCAAGAATATTCACTCGTTGCCCGTCTTTGCGCAATGCGGATCCTTCTCAGGTTCAGTCGAAACTTCGCTTGCTTAGTGATTTGGGTTTAGGCTCAGCTGAGCTTGTAAAGATTATCAATTGTAGGCCTCGATTTTTCAGGACTCGACTTAACCATAATTTCGACGAGAGGCTTGACTCTCTTATGTCATTGTTTGAGTCAAAGGAAATGCTTCATAAGGCCATTGCAAGAAACCCTTCATTGCTGTGTGAAAATAATTATGACATTGAACGTATTGTTAAACAATATGAAGAGTTAGGTATACCGAAAAGGGACTTGGTTCAAATGATGATTTTGCGGCCGACGGTTATTTCAAGAACTTCCTTTGACGATGAGAAGATGGAATATATAAGTAGGACTGGGCTTTCCAAGGATTCAAAATTGTACAAATATGTGGTGACATTAATAGGCATCTCTCGCGTGGAAACAATTCGCGAAAAGGTGTTGAATTTTACAAAGTATGGTTTGTCGGATGATGAGATATTCGGTCTTTTTGGGAAGTCTCCTAATATTTTGACATTGTCAACTGATAAGGTTCAAAGGAACATGACTTTCATTTTAGGCACAATGAAGCTTGAAGCTAACATAATCTTTACGTACCCATATCTGTTGTTTTCAAATATGGAGACTGTTTTGAAGCCAAGAGTGCTTCTAGCAATGAAGGTACAGAATATGGTTCCTAATATGAAAACACCCTCAATACTTAGAGCATTGAGGATGTCCGAGGAGAGGTTTTTCAATACGTTTGTCAGATGCCATGATAAGGAAATTGCTGATGAGTTAATGGAATTTTATAAAAGGACAAAACAGGTTAAGAGATTAGCAGTTTCATCAAGGAATTGGACTACTAGAGGATTCCCTTTCTGA
Protein sequence

>MS.gene020102.t1

MPATYSTKVPAQNEVEMQNVEDKWKDATEVLSKWGCGDDDLARIFTRCPSLRNADPSQVQSKLRLLSDLGLGSAELVKIINCRPRFFRTRLNHNFDERLDSLMSLFESKEMLHKAIARNPSLLCENNYDIERIVKQYEELGIPKRDLVQMMILRPTVISRTSFDDEKMEYISRTGLSKDSKLYKYVVTLIGISRVETIREKVLNFTKYGLSDDEIFGLFGKSPNILTLSTDKVQRNMTFILGTMKLEANIIFTYPYLLFSNMETVLKPRVLLAMKVQNMVPNMKTPSILRALRMSEERFFNTFVRCHDKEIADELMEFYKRTKQVKRLAVSSRNWTTRGFPF