AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene020104

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene020104.t1 MTR_8g012210 95.601 341 15 0 2 342 30 370 0.0 677
MS.gene020104.t1 MTR_2g437260 20.130 308 233 9 35 335 80 381 5.11e-12 66.6
MS.gene020104.t1 MTR_4g120380 21.498 307 226 8 19 319 72 369 5.70e-12 66.6
MS.gene020104.t1 MTR_2g436460 21.212 297 218 9 30 319 86 373 1.54e-11 65.1
MS.gene020104.t1 MTR_6g083110 56.364 55 20 1 244 298 1 51 2.31e-11 62.0
MS.gene020104.t1 MTR_4g120380 20.521 307 230 7 19 319 72 370 2.86e-11 64.7
MS.gene020104.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.gene020104.t1 AT1G79220 48.485 330 165 3 16 342 72 399 1.16e-105 315
MS.gene020104.t1 AT1G21150 22.047 254 194 4 20 269 47 300 4.02e-11 63.9
MS.gene020104.t1 AT1G21150 22.047 254 194 4 20 269 83 336 4.19e-11 63.9
MS.gene020104.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:+77089614 MS.gene020104:CDS
GTTGACAATGTCAAAATATT+AGG 0.276459 8.3:-77090095 None:intergenic
CTTCGCTTGCTTAGTGATTT+GGG 0.280618 8.3:+77089615 MS.gene020104:CDS
GGAAATTGCTGATGAGTTAA+TGG 0.297355 8.3:+77090355 MS.gene020104:CDS
TTGCTTAGTGATTTGGGTTT+AGG 0.299185 8.3:+77089621 MS.gene020104:CDS
AAATATGTGGTGACATTAAT+AGG 0.301744 8.3:+77089978 MS.gene020104:CDS
TAGCAGTTTCATCAAGGAAT+TGG 0.311012 8.3:+77090411 MS.gene020104:CDS
CAAGCCTCTCGTCGAAATTA+TGG 0.312035 8.3:-77089704 None:intergenic
AGCAATGAAGGTACAGAATA+TGG 0.327499 8.3:+77090244 MS.gene020104:CDS
GTTAAACAATATGAAGAGTT+AGG 0.347136 8.3:+77089828 MS.gene020104:CDS
ATATTTGAAAACAACAGATA+TGG 0.357754 8.3:-77090191 None:intergenic
TTTGACATTGTCAACTGATA+AGG 0.368653 8.3:+77090103 MS.gene020104:CDS
TGCAAAATGTTGAAGACAAA+TGG 0.380077 8.3:+77089478 MS.gene020104:CDS
TTCATTGCTAGAAGCACTCT+TGG 0.407140 8.3:-77090230 None:intergenic
GCGCAATGCGGATCCTTCTC+AGG 0.407457 8.3:+77089581 MS.gene020104:CDS
TATGTCATTGTTTGAGTCAA+AGG 0.408420 8.3:+77089734 MS.gene020104:CDS
TTGTAAAGATTATCAATTGT+AGG 0.408436 8.3:+77089655 MS.gene020104:CDS
CATCAGCAATTTCCTTATCA+TGG 0.411377 8.3:-77090346 None:intergenic
TTGTCGGATGATGAGATATT+CGG 0.417333 8.3:+77090056 MS.gene020104:CDS
CGTGGAAACAATTCGCGAAA+AGG 0.422845 8.3:+77090010 MS.gene020104:CDS
AGCTGGGACTTTCGTCGAAT+AGG 0.432888 8.3:-77089439 None:intergenic
CCTCAATGCTCTAAGTATTG+AGG 0.451275 8.3:-77090285 None:intergenic
CTCAATGCTCTAAGTATTGA+GGG 0.456627 8.3:-77090284 None:intergenic
TTCCTTTGACGATGAGAAGA+TGG 0.459653 8.3:+77089911 MS.gene020104:CDS
ATGGAATATATAAGTAGGAC+TGG 0.464288 8.3:+77089930 MS.gene020104:CDS
AAGAGTTAGGTATACCGAAA+AGG 0.464523 8.3:+77089841 MS.gene020104:CDS
GTCAAAGGAAATGCTTCATA+AGG 0.473131 8.3:+77089749 MS.gene020104:CDS
GATCCGCATTGCGCAAAGAC+GGG 0.492040 8.3:-77089572 None:intergenic
GGGTTGTGGTGATGACGATT+TGG 0.493364 8.3:+77089530 MS.gene020104:CDS
ATATAAAAGTAGTTCAGAAA+GGG 0.499107 8.3:-77090448 None:intergenic
AGAGTTAGGTATACCGAAAA+GGG 0.502937 8.3:+77089842 MS.gene020104:CDS
TTCAAAATTGTACAAATATG+TGG 0.504006 8.3:+77089965 MS.gene020104:CDS
GTTTGTCAGATGCCATGATA+AGG 0.508257 8.3:+77090334 MS.gene020104:CDS
AGGTATACCGAAAAGGGACT+TGG 0.508376 8.3:+77089848 MS.gene020104:CDS
TATTTGAAAACAACAGATAT+GGG 0.512551 8.3:-77090190 None:intergenic
AATATAAAAGTAGTTCAGAA+AGG 0.519070 8.3:-77090449 None:intergenic
GGATCCGCATTGCGCAAAGA+CGG 0.525836 8.3:-77089573 None:intergenic
AGAGATTAGCAGTTTCATCA+AGG 0.527319 8.3:+77090405 MS.gene020104:CDS
AAGAGTGCTTCTAGCAATGA+AGG 0.527541 8.3:+77090232 MS.gene020104:CDS
CAATGAAGGGTTTCTTGCAA+TGG 0.534493 8.3:-77089772 None:intergenic
AGAAGATGGAATATATAAGT+AGG 0.535407 8.3:+77089925 MS.gene020104:CDS
TTCCATCTTCTCATCGTCAA+AGG 0.562047 8.3:-77089913 None:intergenic
AAGTAGGACTGGGCTTTCCA+AGG 0.567180 8.3:+77089941 MS.gene020104:CDS
TCAAGGAATTGGACTACTAG+AGG 0.573509 8.3:+77090422 MS.gene020104:CDS
CATTGAGGATGTCCGAGGAG+AGG 0.582695 8.3:+77090300 MS.gene020104:CDS
ACTTTCGTCGAATAGGTGGC+AGG 0.582772 8.3:-77089432 None:intergenic
ATTAATAGGCATCTCTCGCG+TGG 0.592649 8.3:+77089992 MS.gene020104:CDS
TGTCAACTGATAAGGTTCAA+AGG 0.601835 8.3:+77090111 MS.gene020104:CDS
GAAAGTCCCAGCTCAAAATG+AGG 0.604863 8.3:+77089449 MS.gene020104:CDS
CCTCAATACTTAGAGCATTG+AGG 0.607754 8.3:+77090285 MS.gene020104:CDS
TGGAATATATAAGTAGGACT+GGG 0.608434 8.3:+77089931 MS.gene020104:CDS
TGGGACTTTCGTCGAATAGG+TGG 0.610226 8.3:-77089436 None:intergenic
TTAACCATAATTTCGACGAG+AGG 0.625796 8.3:+77089700 MS.gene020104:CDS
AGTTTCGACTGAACCTGAGA+AGG 0.646506 8.3:-77089594 None:intergenic
AAATGTTGAAGACAAATGGA+AGG 0.655802 8.3:+77089482 MS.gene020104:CDS
GAAGTTCTTGAAATAACCGT+CGG 0.665623 8.3:-77089891 None:intergenic
TAGAGCATTGAGGATGTCCG+AGG 0.681763 8.3:+77090295 MS.gene020104:CDS
TTGCCCGTCTTTGCGCAATG+CGG 0.689638 8.3:+77089569 MS.gene020104:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! AGTTAATGGAATTTTATAAA+AGG + chr8.3:77090369-77090388 MS.gene020104:CDS 15.0%
!! ATATTTGAAAACAACAGATA+TGG - chr8.3:77090194-77090213 None:intergenic 20.0%
!! TATTTGAAAACAACAGATAT+GGG - chr8.3:77090193-77090212 None:intergenic 20.0%
!! TTCAAAATTGTACAAATATG+TGG + chr8.3:77089965-77089984 MS.gene020104:CDS 20.0%
!! TTGTAAAGATTATCAATTGT+AGG + chr8.3:77089655-77089674 MS.gene020104:CDS 20.0%
!!! ATATCTGTTGTTTTCAAATA+TGG + chr8.3:77090193-77090212 MS.gene020104:CDS 20.0%
!!! ATTTTATAAAAGGACAAAAC+AGG + chr8.3:77090379-77090398 MS.gene020104:CDS 20.0%
! AAATATGTGGTGACATTAAT+AGG + chr8.3:77089978-77089997 MS.gene020104:CDS 25.0%
! AGAAGATGGAATATATAAGT+AGG + chr8.3:77089925-77089944 MS.gene020104:CDS 25.0%
! GTTAAACAATATGAAGAGTT+AGG + chr8.3:77089828-77089847 MS.gene020104:CDS 25.0%
! GTTGACAATGTCAAAATATT+AGG - chr8.3:77090098-77090117 None:intergenic 25.0%
!! GTGTTGAATTTTACAAAGTA+TGG + chr8.3:77090032-77090051 MS.gene020104:CDS 25.0%
!! TTTGTACAATTTTGAATCCT+TGG - chr8.3:77089961-77089980 None:intergenic 25.0%
!!! TACTGAAGTTTTGAGTAAAT+GGG + chr8.3:77089509-77089528 MS.gene020104:CDS 25.0%
!!! TTTTACAAAGTATGGTTTGT+CGG + chr8.3:77090040-77090059 MS.gene020104:CDS 25.0%
AAATGTTGAAGACAAATGGA+AGG + chr8.3:77089482-77089501 MS.gene020104:CDS 30.0%
ATGGAATATATAAGTAGGAC+TGG + chr8.3:77089930-77089949 MS.gene020104:CDS 30.0%
TATGTCATTGTTTGAGTCAA+AGG + chr8.3:77089734-77089753 MS.gene020104:CDS 30.0%
TGCAAAATGTTGAAGACAAA+TGG + chr8.3:77089478-77089497 MS.gene020104:CDS 30.0%
TGGAATATATAAGTAGGACT+GGG + chr8.3:77089931-77089950 MS.gene020104:CDS 30.0%
TTTGACATTGTCAACTGATA+AGG + chr8.3:77090103-77090122 MS.gene020104:CDS 30.0%
! AGGAACATGACTTTCATTTT+AGG + chr8.3:77090131-77090150 MS.gene020104:CDS 30.0%
! ATGAGATATTCGGTCTTTTT+GGG + chr8.3:77090066-77090085 MS.gene020104:CDS 30.0%
! TATTTTCACACAGCAATGAA+GGG - chr8.3:77089788-77089807 None:intergenic 30.0%
! TGGTTCAAATGATGATTTTG+CGG + chr8.3:77089868-77089887 MS.gene020104:CDS 30.0%
! TTATTTTCACACAGCAATGA+AGG - chr8.3:77089789-77089808 None:intergenic 30.0%
!!! ACTGAAGTTTTGAGTAAATG+GGG + chr8.3:77089510-77089529 MS.gene020104:CDS 30.0%
!!! ATTGAGGGTGTTTTCATATT+AGG - chr8.3:77090272-77090291 None:intergenic 30.0%
!!! CTACTGAAGTTTTGAGTAAA+TGG + chr8.3:77089508-77089527 MS.gene020104:CDS 30.0%
AAGAGTTAGGTATACCGAAA+AGG + chr8.3:77089841-77089860 MS.gene020104:CDS 35.0%
AGAGATTAGCAGTTTCATCA+AGG + chr8.3:77090405-77090424 MS.gene020104:CDS 35.0%
AGAGTTAGGTATACCGAAAA+GGG + chr8.3:77089842-77089861 MS.gene020104:CDS 35.0%
CATCAGCAATTTCCTTATCA+TGG - chr8.3:77090349-77090368 None:intergenic 35.0%
GAAGTTCTTGAAATAACCGT+CGG - chr8.3:77089894-77089913 None:intergenic 35.0%
GGAAATTGCTGATGAGTTAA+TGG + chr8.3:77090355-77090374 MS.gene020104:CDS 35.0%
GTCAAAGGAAATGCTTCATA+AGG + chr8.3:77089749-77089768 MS.gene020104:CDS 35.0%
TAGCAGTTTCATCAAGGAAT+TGG + chr8.3:77090411-77090430 MS.gene020104:CDS 35.0%
TGTCAACTGATAAGGTTCAA+AGG + chr8.3:77090111-77090130 MS.gene020104:CDS 35.0%
TTAACCATAATTTCGACGAG+AGG + chr8.3:77089700-77089719 MS.gene020104:CDS 35.0%
TTGTCGGATGATGAGATATT+CGG + chr8.3:77090056-77090075 MS.gene020104:CDS 35.0%
! AGCAATGAAGGTACAGAATA+TGG + chr8.3:77090244-77090263 MS.gene020104:CDS 35.0%
! ATTTCAACCTCATTTTGAGC+TGG - chr8.3:77089459-77089478 None:intergenic 35.0%
! ATTTGAACCAAGTCCCTTTT+CGG - chr8.3:77089858-77089877 None:intergenic 35.0%
! GATGAGATATTCGGTCTTTT+TGG + chr8.3:77090065-77090084 MS.gene020104:CDS 35.0%
! TTGCTTAGTGATTTGGGTTT+AGG + chr8.3:77089621-77089640 MS.gene020104:CDS 35.0%
! TTTCAACCTCATTTTGAGCT+GGG - chr8.3:77089458-77089477 None:intergenic 35.0%
!! CTCAATGCTCTAAGTATTGA+GGG - chr8.3:77090287-77090306 None:intergenic 35.0%
ACTTCGCTTGCTTAGTGATT+TGG + chr8.3:77089614-77089633 MS.gene020104:CDS 40.0%
CAATGAAGGGTTTCTTGCAA+TGG - chr8.3:77089775-77089794 None:intergenic 40.0%
CGTATTGAAAAACCTCTCCT+CGG - chr8.3:77090315-77090334 None:intergenic 40.0%
CTTCGCTTGCTTAGTGATTT+GGG + chr8.3:77089615-77089634 MS.gene020104:CDS 40.0%
GTTTGTCAGATGCCATGATA+AGG + chr8.3:77090334-77090353 MS.gene020104:CDS 40.0%
TCAAGGAATTGGACTACTAG+AGG + chr8.3:77090422-77090441 MS.gene020104:CDS 40.0%
TTCCATCTTCTCATCGTCAA+AGG - chr8.3:77089916-77089935 None:intergenic 40.0%
TTCCTTTGACGATGAGAAGA+TGG + chr8.3:77089911-77089930 MS.gene020104:CDS 40.0%
! ATTGTAGGCCTCGATTTTTC+AGG + chr8.3:77089670-77089689 MS.gene020104:CDS 40.0%
! CCTCAATGCTCTAAGTATTG+AGG - chr8.3:77090288-77090307 None:intergenic 40.0%
!! AAGAGTGCTTCTAGCAATGA+AGG + chr8.3:77090232-77090251 MS.gene020104:CDS 40.0%
!! CCTCAATACTTAGAGCATTG+AGG + chr8.3:77090285-77090304 MS.gene020104:CDS 40.0%
!! GTTTTGAGTAAATGGGGTTG+TGG + chr8.3:77089516-77089535 MS.gene020104:CDS 40.0%
!! TTCATTGCTAGAAGCACTCT+TGG - chr8.3:77090233-77090252 None:intergenic 40.0%
AGGTATACCGAAAAGGGACT+TGG + chr8.3:77089848-77089867 MS.gene020104:CDS 45.0%
AGTCGAGTCCTGAAAAATCG+AGG - chr8.3:77089681-77089700 None:intergenic 45.0%
AGTTTCGACTGAACCTGAGA+AGG - chr8.3:77089597-77089616 None:intergenic 45.0%
ATTAATAGGCATCTCTCGCG+TGG + chr8.3:77089992-77090011 MS.gene020104:CDS 45.0%
CAAGCCTCTCGTCGAAATTA+TGG - chr8.3:77089707-77089726 None:intergenic 45.0%
CGTGGAAACAATTCGCGAAA+AGG + chr8.3:77090010-77090029 MS.gene020104:CDS 45.0%
GAAAGTCCCAGCTCAAAATG+AGG + chr8.3:77089449-77089468 MS.gene020104:CDS 45.0%
! AATGATGATTTTGCGGCCGA+CGG + chr8.3:77089875-77089894 MS.gene020104:CDS 45.0%
AAGTAGGACTGGGCTTTCCA+AGG + chr8.3:77089941-77089960 MS.gene020104:CDS 50.0%
ACTTTCGTCGAATAGGTGGC+AGG - chr8.3:77089435-77089454 None:intergenic 50.0%
AGCTGGGACTTTCGTCGAAT+AGG - chr8.3:77089442-77089461 None:intergenic 50.0%
TGGGACTTTCGTCGAATAGG+TGG - chr8.3:77089439-77089458 None:intergenic 50.0%
! GGGTTGTGGTGATGACGATT+TGG + chr8.3:77089530-77089549 MS.gene020104:CDS 50.0%
!! TAGAGCATTGAGGATGTCCG+AGG + chr8.3:77090295-77090314 MS.gene020104:CDS 50.0%
CATTGAGGATGTCCGAGGAG+AGG + chr8.3:77090300-77090319 MS.gene020104:CDS 55.0%
GATCCGCATTGCGCAAAGAC+GGG - chr8.3:77089575-77089594 None:intergenic 55.0%
GGATCCGCATTGCGCAAAGA+CGG - chr8.3:77089576-77089595 None:intergenic 55.0%
TTGCCCGTCTTTGCGCAATG+CGG + chr8.3:77089569-77089588 MS.gene020104:CDS 55.0%
GCGCAATGCGGATCCTTCTC+AGG + chr8.3:77089581-77089600 MS.gene020104:CDS 60.0%


Chromosome Type Strat End Strand Name
chr8.3 gene 77089429 77090457 77089429 ID=MS.gene020104
chr8.3 mRNA 77089429 77090457 77089429 ID=MS.gene020104.t1;Parent=MS.gene020104
chr8.3 exon 77089429 77090457 77089429 ID=MS.gene020104.t1.exon1;Parent=MS.gene020104.t1
chr8.3 CDS 77089429 77090457 77089429 ID=cds.MS.gene020104.t1;Parent=MS.gene020104.t1
Gene Sequence

>MS.gene020104

ATGCCTGCCACCTATTCGACGAAAGTCCCAGCTCAAAATGAGGTTGAAATGCAAAATGTTGAAGACAAATGGAAGGATGCTACTGAAGTTTTGAGTAAATGGGGTTGTGGTGATGACGATTTGGCAAGAATATTCACTCGTTGCCCGTCTTTGCGCAATGCGGATCCTTCTCAGGTTCAGTCGAAACTTCGCTTGCTTAGTGATTTGGGTTTAGGCTCAGCTGAGCTTGTAAAGATTATCAATTGTAGGCCTCGATTTTTCAGGACTCGACTTAACCATAATTTCGACGAGAGGCTTGACTCTCTTATGTCATTGTTTGAGTCAAAGGAAATGCTTCATAAGGCCATTGCAAGAAACCCTTCATTGCTGTGTGAAAATAATTATGACATTGAACGTATTGTTAAACAATATGAAGAGTTAGGTATACCGAAAAGGGACTTGGTTCAAATGATGATTTTGCGGCCGACGGTTATTTCAAGAACTTCCTTTGACGATGAGAAGATGGAATATATAAGTAGGACTGGGCTTTCCAAGGATTCAAAATTGTACAAATATGTGGTGACATTAATAGGCATCTCTCGCGTGGAAACAATTCGCGAAAAGGTGTTGAATTTTACAAAGTATGGTTTGTCGGATGATGAGATATTCGGTCTTTTTGGGAAGTCTCCTAATATTTTGACATTGTCAACTGATAAGGTTCAAAGGAACATGACTTTCATTTTAGGCACAATGAAGCTTGAAGCTAACATAATCTTTACGTACCCATATCTGTTGTTTTCAAATATGGAGACTGTTTTGAAGCCAAGAGTGCTTCTAGCAATGAAGGTACAGAATATGGTTCCTAATATGAAAACACCCTCAATACTTAGAGCATTGAGGATGTCCGAGGAGAGGTTTTTCAATACGTTTGTCAGATGCCATGATAAGGAAATTGCTGATGAGTTAATGGAATTTTATAAAAGGACAAAACAGGTTAAGAGATTAGCAGTTTCATCAAGGAATTGGACTACTAGAGGATTCCCTTTCTGA
Protein sequence

>MS.gene020104.t1

MPATYSTKVPAQNEVEMQNVEDKWKDATEVLSKWGCGDDDLARIFTRCPSLRNADPSQVQSKLRLLSDLGLGSAELVKIINCRPRFFRTRLNHNFDERLDSLMSLFESKEMLHKAIARNPSLLCENNYDIERIVKQYEELGIPKRDLVQMMILRPTVISRTSFDDEKMEYISRTGLSKDSKLYKYVVTLIGISRVETIREKVLNFTKYGLSDDEIFGLFGKSPNILTLSTDKVQRNMTFILGTMKLEANIIFTYPYLLFSNMETVLKPRVLLAMKVQNMVPNMKTPSILRALRMSEERFFNTFVRCHDKEIADELMEFYKRTKQVKRLAVSSRNWTTRGFPF