AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene020109

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene020109.t1 MTR_8g012210 95.601 341 15 0 2 342 30 370 0.0 677
MS.gene020109.t1 MTR_2g437260 20.130 308 233 9 35 335 80 381 5.11e-12 66.6
MS.gene020109.t1 MTR_4g120380 21.498 307 226 8 19 319 72 369 5.70e-12 66.6
MS.gene020109.t1 MTR_2g436460 21.212 297 218 9 30 319 86 373 1.54e-11 65.1
MS.gene020109.t1 MTR_6g083110 56.364 55 20 1 244 298 1 51 2.31e-11 62.0
MS.gene020109.t1 MTR_4g120380 20.521 307 230 7 19 319 72 370 2.86e-11 64.7
MS.gene020109.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.gene020109.t1 AT1G79220 48.485 330 165 3 16 342 72 399 1.16e-105 315
MS.gene020109.t1 AT1G21150 22.047 254 194 4 20 269 47 300 4.02e-11 63.9
MS.gene020109.t1 AT1G21150 22.047 254 194 4 20 269 83 336 4.19e-11 63.9
MS.gene020109.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:+77307519 MS.gene020109:CDS
GTTGACAATGTCAAAATATT+AGG 0.276459 8.3:-77308000 None:intergenic
CTTCGCTTGCTTAGTGATTT+GGG 0.280618 8.3:+77307520 MS.gene020109:CDS
GGAAATTGCTGATGAGTTAA+TGG 0.297355 8.3:+77308260 MS.gene020109:CDS
TTGCTTAGTGATTTGGGTTT+AGG 0.299185 8.3:+77307526 MS.gene020109:CDS
AAATATGTGGTGACATTAAT+AGG 0.301744 8.3:+77307883 MS.gene020109:CDS
TAGCAGTTTCATCAAGGAAT+TGG 0.311012 8.3:+77308316 MS.gene020109:CDS
CAAGCCTCTCGTCGAAATTA+TGG 0.312035 8.3:-77307609 None:intergenic
AGCAATGAAGGTACAGAATA+TGG 0.327499 8.3:+77308149 MS.gene020109:CDS
GTTAAACAATATGAAGAGTT+AGG 0.347136 8.3:+77307733 MS.gene020109:CDS
ATATTTGAAAACAACAGATA+TGG 0.357754 8.3:-77308096 None:intergenic
TTTGACATTGTCAACTGATA+AGG 0.368653 8.3:+77308008 MS.gene020109:CDS
TGCAAAATGTTGAAGACAAA+TGG 0.380077 8.3:+77307383 MS.gene020109:CDS
TTCATTGCTAGAAGCACTCT+TGG 0.407140 8.3:-77308135 None:intergenic
GCGCAATGCGGATCCTTCTC+AGG 0.407457 8.3:+77307486 MS.gene020109:CDS
TATGTCATTGTTTGAGTCAA+AGG 0.408420 8.3:+77307639 MS.gene020109:CDS
TTGTAAAGATTATCAATTGT+AGG 0.408436 8.3:+77307560 MS.gene020109:CDS
CATCAGCAATTTCCTTATCA+TGG 0.411377 8.3:-77308251 None:intergenic
TTGTCGGATGATGAGATATT+CGG 0.417333 8.3:+77307961 MS.gene020109:CDS
CGTGGAAACAATTCGCGAAA+AGG 0.422845 8.3:+77307915 MS.gene020109:CDS
AGCTGGGACTTTCGTCGAAT+AGG 0.432888 8.3:-77307344 None:intergenic
CCTCAATGCTCTAAGTATTG+AGG 0.451275 8.3:-77308190 None:intergenic
CTCAATGCTCTAAGTATTGA+GGG 0.456627 8.3:-77308189 None:intergenic
TTCCTTTGACGATGAGAAGA+TGG 0.459653 8.3:+77307816 MS.gene020109:CDS
ATGGAATATATAAGTAGGAC+TGG 0.464288 8.3:+77307835 MS.gene020109:CDS
AAGAGTTAGGTATACCGAAA+AGG 0.464523 8.3:+77307746 MS.gene020109:CDS
GTCAAAGGAAATGCTTCATA+AGG 0.473131 8.3:+77307654 MS.gene020109:CDS
GATCCGCATTGCGCAAAGAC+GGG 0.492040 8.3:-77307477 None:intergenic
GGGTTGTGGTGATGACGATT+TGG 0.493364 8.3:+77307435 MS.gene020109:CDS
ATATAAAAGTAGTTCAGAAA+GGG 0.499107 8.3:-77308353 None:intergenic
AGAGTTAGGTATACCGAAAA+GGG 0.502937 8.3:+77307747 MS.gene020109:CDS
TTCAAAATTGTACAAATATG+TGG 0.504006 8.3:+77307870 MS.gene020109:CDS
GTTTGTCAGATGCCATGATA+AGG 0.508257 8.3:+77308239 MS.gene020109:CDS
AGGTATACCGAAAAGGGACT+TGG 0.508376 8.3:+77307753 MS.gene020109:CDS
TATTTGAAAACAACAGATAT+GGG 0.512551 8.3:-77308095 None:intergenic
AATATAAAAGTAGTTCAGAA+AGG 0.519070 8.3:-77308354 None:intergenic
GGATCCGCATTGCGCAAAGA+CGG 0.525836 8.3:-77307478 None:intergenic
AGAGATTAGCAGTTTCATCA+AGG 0.527319 8.3:+77308310 MS.gene020109:CDS
AAGAGTGCTTCTAGCAATGA+AGG 0.527541 8.3:+77308137 MS.gene020109:CDS
CAATGAAGGGTTTCTTGCAA+TGG 0.534493 8.3:-77307677 None:intergenic
AGAAGATGGAATATATAAGT+AGG 0.535407 8.3:+77307830 MS.gene020109:CDS
TTCCATCTTCTCATCGTCAA+AGG 0.562047 8.3:-77307818 None:intergenic
AAGTAGGACTGGGCTTTCCA+AGG 0.567180 8.3:+77307846 MS.gene020109:CDS
TCAAGGAATTGGACTACTAG+AGG 0.573509 8.3:+77308327 MS.gene020109:CDS
CATTGAGGATGTCCGAGGAG+AGG 0.582695 8.3:+77308205 MS.gene020109:CDS
ACTTTCGTCGAATAGGTGGC+AGG 0.582772 8.3:-77307337 None:intergenic
ATTAATAGGCATCTCTCGCG+TGG 0.592649 8.3:+77307897 MS.gene020109:CDS
TGTCAACTGATAAGGTTCAA+AGG 0.601835 8.3:+77308016 MS.gene020109:CDS
GAAAGTCCCAGCTCAAAATG+AGG 0.604863 8.3:+77307354 MS.gene020109:CDS
CCTCAATACTTAGAGCATTG+AGG 0.607754 8.3:+77308190 MS.gene020109:CDS
TGGAATATATAAGTAGGACT+GGG 0.608434 8.3:+77307836 MS.gene020109:CDS
TGGGACTTTCGTCGAATAGG+TGG 0.610226 8.3:-77307341 None:intergenic
TTAACCATAATTTCGACGAG+AGG 0.625796 8.3:+77307605 MS.gene020109:CDS
AGTTTCGACTGAACCTGAGA+AGG 0.646506 8.3:-77307499 None:intergenic
AAATGTTGAAGACAAATGGA+AGG 0.655802 8.3:+77307387 MS.gene020109:CDS
GAAGTTCTTGAAATAACCGT+CGG 0.665623 8.3:-77307796 None:intergenic
TAGAGCATTGAGGATGTCCG+AGG 0.681763 8.3:+77308200 MS.gene020109:CDS
TTGCCCGTCTTTGCGCAATG+CGG 0.689638 8.3:+77307474 MS.gene020109:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! AGTTAATGGAATTTTATAAA+AGG + chr8.3:77308274-77308293 MS.gene020109:CDS 15.0%
!! ATATTTGAAAACAACAGATA+TGG - chr8.3:77308099-77308118 None:intergenic 20.0%
!! TATTTGAAAACAACAGATAT+GGG - chr8.3:77308098-77308117 None:intergenic 20.0%
!! TTCAAAATTGTACAAATATG+TGG + chr8.3:77307870-77307889 MS.gene020109:CDS 20.0%
!! TTGTAAAGATTATCAATTGT+AGG + chr8.3:77307560-77307579 MS.gene020109:CDS 20.0%
!!! ATATCTGTTGTTTTCAAATA+TGG + chr8.3:77308098-77308117 MS.gene020109:CDS 20.0%
!!! ATTTTATAAAAGGACAAAAC+AGG + chr8.3:77308284-77308303 MS.gene020109:CDS 20.0%
! AAATATGTGGTGACATTAAT+AGG + chr8.3:77307883-77307902 MS.gene020109:CDS 25.0%
! AGAAGATGGAATATATAAGT+AGG + chr8.3:77307830-77307849 MS.gene020109:CDS 25.0%
! GTTAAACAATATGAAGAGTT+AGG + chr8.3:77307733-77307752 MS.gene020109:CDS 25.0%
! GTTGACAATGTCAAAATATT+AGG - chr8.3:77308003-77308022 None:intergenic 25.0%
!! GTGTTGAATTTTACAAAGTA+TGG + chr8.3:77307937-77307956 MS.gene020109:CDS 25.0%
!! TTTGTACAATTTTGAATCCT+TGG - chr8.3:77307866-77307885 None:intergenic 25.0%
!!! TACTGAAGTTTTGAGTAAAT+GGG + chr8.3:77307414-77307433 MS.gene020109:CDS 25.0%
!!! TTTTACAAAGTATGGTTTGT+CGG + chr8.3:77307945-77307964 MS.gene020109:CDS 25.0%
AAATGTTGAAGACAAATGGA+AGG + chr8.3:77307387-77307406 MS.gene020109:CDS 30.0%
ATGGAATATATAAGTAGGAC+TGG + chr8.3:77307835-77307854 MS.gene020109:CDS 30.0%
TATGTCATTGTTTGAGTCAA+AGG + chr8.3:77307639-77307658 MS.gene020109:CDS 30.0%
TGCAAAATGTTGAAGACAAA+TGG + chr8.3:77307383-77307402 MS.gene020109:CDS 30.0%
TGGAATATATAAGTAGGACT+GGG + chr8.3:77307836-77307855 MS.gene020109:CDS 30.0%
TTTGACATTGTCAACTGATA+AGG + chr8.3:77308008-77308027 MS.gene020109:CDS 30.0%
! AGGAACATGACTTTCATTTT+AGG + chr8.3:77308036-77308055 MS.gene020109:CDS 30.0%
! ATGAGATATTCGGTCTTTTT+GGG + chr8.3:77307971-77307990 MS.gene020109:CDS 30.0%
! TATTTTCACACAGCAATGAA+GGG - chr8.3:77307693-77307712 None:intergenic 30.0%
! TGGTTCAAATGATGATTTTG+CGG + chr8.3:77307773-77307792 MS.gene020109:CDS 30.0%
! TTATTTTCACACAGCAATGA+AGG - chr8.3:77307694-77307713 None:intergenic 30.0%
!!! ACTGAAGTTTTGAGTAAATG+GGG + chr8.3:77307415-77307434 MS.gene020109:CDS 30.0%
!!! ATTGAGGGTGTTTTCATATT+AGG - chr8.3:77308177-77308196 None:intergenic 30.0%
!!! CTACTGAAGTTTTGAGTAAA+TGG + chr8.3:77307413-77307432 MS.gene020109:CDS 30.0%
AAGAGTTAGGTATACCGAAA+AGG + chr8.3:77307746-77307765 MS.gene020109:CDS 35.0%
AGAGATTAGCAGTTTCATCA+AGG + chr8.3:77308310-77308329 MS.gene020109:CDS 35.0%
AGAGTTAGGTATACCGAAAA+GGG + chr8.3:77307747-77307766 MS.gene020109:CDS 35.0%
CATCAGCAATTTCCTTATCA+TGG - chr8.3:77308254-77308273 None:intergenic 35.0%
GAAGTTCTTGAAATAACCGT+CGG - chr8.3:77307799-77307818 None:intergenic 35.0%
GGAAATTGCTGATGAGTTAA+TGG + chr8.3:77308260-77308279 MS.gene020109:CDS 35.0%
GTCAAAGGAAATGCTTCATA+AGG + chr8.3:77307654-77307673 MS.gene020109:CDS 35.0%
TAGCAGTTTCATCAAGGAAT+TGG + chr8.3:77308316-77308335 MS.gene020109:CDS 35.0%
TGTCAACTGATAAGGTTCAA+AGG + chr8.3:77308016-77308035 MS.gene020109:CDS 35.0%
TTAACCATAATTTCGACGAG+AGG + chr8.3:77307605-77307624 MS.gene020109:CDS 35.0%
TTGTCGGATGATGAGATATT+CGG + chr8.3:77307961-77307980 MS.gene020109:CDS 35.0%
! AGCAATGAAGGTACAGAATA+TGG + chr8.3:77308149-77308168 MS.gene020109:CDS 35.0%
! ATTTCAACCTCATTTTGAGC+TGG - chr8.3:77307364-77307383 None:intergenic 35.0%
! ATTTGAACCAAGTCCCTTTT+CGG - chr8.3:77307763-77307782 None:intergenic 35.0%
! GATGAGATATTCGGTCTTTT+TGG + chr8.3:77307970-77307989 MS.gene020109:CDS 35.0%
! TTGCTTAGTGATTTGGGTTT+AGG + chr8.3:77307526-77307545 MS.gene020109:CDS 35.0%
! TTTCAACCTCATTTTGAGCT+GGG - chr8.3:77307363-77307382 None:intergenic 35.0%
!! CTCAATGCTCTAAGTATTGA+GGG - chr8.3:77308192-77308211 None:intergenic 35.0%
ACTTCGCTTGCTTAGTGATT+TGG + chr8.3:77307519-77307538 MS.gene020109:CDS 40.0%
CAATGAAGGGTTTCTTGCAA+TGG - chr8.3:77307680-77307699 None:intergenic 40.0%
CGTATTGAAAAACCTCTCCT+CGG - chr8.3:77308220-77308239 None:intergenic 40.0%
CTTCGCTTGCTTAGTGATTT+GGG + chr8.3:77307520-77307539 MS.gene020109:CDS 40.0%
GTTTGTCAGATGCCATGATA+AGG + chr8.3:77308239-77308258 MS.gene020109:CDS 40.0%
TCAAGGAATTGGACTACTAG+AGG + chr8.3:77308327-77308346 MS.gene020109:CDS 40.0%
TTCCATCTTCTCATCGTCAA+AGG - chr8.3:77307821-77307840 None:intergenic 40.0%
TTCCTTTGACGATGAGAAGA+TGG + chr8.3:77307816-77307835 MS.gene020109:CDS 40.0%
! ATTGTAGGCCTCGATTTTTC+AGG + chr8.3:77307575-77307594 MS.gene020109:CDS 40.0%
! CCTCAATGCTCTAAGTATTG+AGG - chr8.3:77308193-77308212 None:intergenic 40.0%
!! AAGAGTGCTTCTAGCAATGA+AGG + chr8.3:77308137-77308156 MS.gene020109:CDS 40.0%
!! CCTCAATACTTAGAGCATTG+AGG + chr8.3:77308190-77308209 MS.gene020109:CDS 40.0%
!! GTTTTGAGTAAATGGGGTTG+TGG + chr8.3:77307421-77307440 MS.gene020109:CDS 40.0%
!! TTCATTGCTAGAAGCACTCT+TGG - chr8.3:77308138-77308157 None:intergenic 40.0%
AGGTATACCGAAAAGGGACT+TGG + chr8.3:77307753-77307772 MS.gene020109:CDS 45.0%
AGTCGAGTCCTGAAAAATCG+AGG - chr8.3:77307586-77307605 None:intergenic 45.0%
AGTTTCGACTGAACCTGAGA+AGG - chr8.3:77307502-77307521 None:intergenic 45.0%
ATTAATAGGCATCTCTCGCG+TGG + chr8.3:77307897-77307916 MS.gene020109:CDS 45.0%
CAAGCCTCTCGTCGAAATTA+TGG - chr8.3:77307612-77307631 None:intergenic 45.0%
CGTGGAAACAATTCGCGAAA+AGG + chr8.3:77307915-77307934 MS.gene020109:CDS 45.0%
GAAAGTCCCAGCTCAAAATG+AGG + chr8.3:77307354-77307373 MS.gene020109:CDS 45.0%
! AATGATGATTTTGCGGCCGA+CGG + chr8.3:77307780-77307799 MS.gene020109:CDS 45.0%
AAGTAGGACTGGGCTTTCCA+AGG + chr8.3:77307846-77307865 MS.gene020109:CDS 50.0%
ACTTTCGTCGAATAGGTGGC+AGG - chr8.3:77307340-77307359 None:intergenic 50.0%
AGCTGGGACTTTCGTCGAAT+AGG - chr8.3:77307347-77307366 None:intergenic 50.0%
TGGGACTTTCGTCGAATAGG+TGG - chr8.3:77307344-77307363 None:intergenic 50.0%
! GGGTTGTGGTGATGACGATT+TGG + chr8.3:77307435-77307454 MS.gene020109:CDS 50.0%
!! TAGAGCATTGAGGATGTCCG+AGG + chr8.3:77308200-77308219 MS.gene020109:CDS 50.0%
CATTGAGGATGTCCGAGGAG+AGG + chr8.3:77308205-77308224 MS.gene020109:CDS 55.0%
GATCCGCATTGCGCAAAGAC+GGG - chr8.3:77307480-77307499 None:intergenic 55.0%
GGATCCGCATTGCGCAAAGA+CGG - chr8.3:77307481-77307500 None:intergenic 55.0%
TTGCCCGTCTTTGCGCAATG+CGG + chr8.3:77307474-77307493 MS.gene020109:CDS 55.0%
GCGCAATGCGGATCCTTCTC+AGG + chr8.3:77307486-77307505 MS.gene020109:CDS 60.0%


Chromosome Type Strat End Strand Name
chr8.3 gene 77307334 77308362 77307334 ID=MS.gene020109
chr8.3 mRNA 77307334 77308362 77307334 ID=MS.gene020109.t1;Parent=MS.gene020109
chr8.3 exon 77307334 77308362 77307334 ID=MS.gene020109.t1.exon1;Parent=MS.gene020109.t1
chr8.3 CDS 77307334 77308362 77307334 ID=cds.MS.gene020109.t1;Parent=MS.gene020109.t1
Gene Sequence

>MS.gene020109

ATGCCTGCCACCTATTCGACGAAAGTCCCAGCTCAAAATGAGGTTGAAATGCAAAATGTTGAAGACAAATGGAAGGATGCTACTGAAGTTTTGAGTAAATGGGGTTGTGGTGATGACGATTTGGCAAGAATATTCACTCGTTGCCCGTCTTTGCGCAATGCGGATCCTTCTCAGGTTCAGTCGAAACTTCGCTTGCTTAGTGATTTGGGTTTAGGCTCAGCTGAGCTTGTAAAGATTATCAATTGTAGGCCTCGATTTTTCAGGACTCGACTTAACCATAATTTCGACGAGAGGCTTGACTCTCTTATGTCATTGTTTGAGTCAAAGGAAATGCTTCATAAGGCCATTGCAAGAAACCCTTCATTGCTGTGTGAAAATAATTATGACATTGAACGTATTGTTAAACAATATGAAGAGTTAGGTATACCGAAAAGGGACTTGGTTCAAATGATGATTTTGCGGCCGACGGTTATTTCAAGAACTTCCTTTGACGATGAGAAGATGGAATATATAAGTAGGACTGGGCTTTCCAAGGATTCAAAATTGTACAAATATGTGGTGACATTAATAGGCATCTCTCGCGTGGAAACAATTCGCGAAAAGGTGTTGAATTTTACAAAGTATGGTTTGTCGGATGATGAGATATTCGGTCTTTTTGGGAAGTCTCCTAATATTTTGACATTGTCAACTGATAAGGTTCAAAGGAACATGACTTTCATTTTAGGCACAATGAAGCTTGAAGCTAACATAATCTTTACGTACCCATATCTGTTGTTTTCAAATATGGAGACTGTTTTGAAGCCAAGAGTGCTTCTAGCAATGAAGGTACAGAATATGGTTCCTAATATGAAAACACCCTCAATACTTAGAGCATTGAGGATGTCCGAGGAGAGGTTTTTCAATACGTTTGTCAGATGCCATGATAAGGAAATTGCTGATGAGTTAATGGAATTTTATAAAAGGACAAAACAGGTTAAGAGATTAGCAGTTTCATCAAGGAATTGGACTACTAGAGGATTCCCTTTCTGA
Protein sequence

>MS.gene020109.t1

MPATYSTKVPAQNEVEMQNVEDKWKDATEVLSKWGCGDDDLARIFTRCPSLRNADPSQVQSKLRLLSDLGLGSAELVKIINCRPRFFRTRLNHNFDERLDSLMSLFESKEMLHKAIARNPSLLCENNYDIERIVKQYEELGIPKRDLVQMMILRPTVISRTSFDDEKMEYISRTGLSKDSKLYKYVVTLIGISRVETIREKVLNFTKYGLSDDEIFGLFGKSPNILTLSTDKVQRNMTFILGTMKLEANIIFTYPYLLFSNMETVLKPRVLLAMKVQNMVPNMKTPSILRALRMSEERFFNTFVRCHDKEIADELMEFYKRTKQVKRLAVSSRNWTTRGFPF