AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene054933

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene054933.t1 MTR_8g012210 95.601 341 15 0 2 342 30 370 0.0 677
MS.gene054933.t1 MTR_2g437260 20.130 308 233 9 35 335 80 381 5.11e-12 66.6
MS.gene054933.t1 MTR_4g120380 21.498 307 226 8 19 319 72 369 5.70e-12 66.6
MS.gene054933.t1 MTR_2g436460 21.212 297 218 9 30 319 86 373 1.54e-11 65.1
MS.gene054933.t1 MTR_6g083110 56.364 55 20 1 244 298 1 51 2.31e-11 62.0
MS.gene054933.t1 MTR_4g120380 20.521 307 230 7 19 319 72 370 2.86e-11 64.7
MS.gene054933.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.gene054933.t1 AT1G79220 48.485 330 165 3 16 342 72 399 1.16e-105 315
MS.gene054933.t1 AT1G21150 22.047 254 194 4 20 269 47 300 4.02e-11 63.9
MS.gene054933.t1 AT1G21150 22.047 254 194 4 20 269 83 336 4.19e-11 63.9
MS.gene054933.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 8.4:-77440565 MS.gene054933:CDS
GTTGACAATGTCAAAATATT+AGG 0.276459 8.4:+77440084 None:intergenic
CTTCGCTTGCTTAGTGATTT+GGG 0.280618 8.4:-77440564 MS.gene054933:CDS
GGAAATTGCTGATGAGTTAA+TGG 0.297355 8.4:-77439824 MS.gene054933:CDS
TTGCTTAGTGATTTGGGTTT+AGG 0.299185 8.4:-77440558 MS.gene054933:CDS
AAATATGTGGTGACATTAAT+AGG 0.301744 8.4:-77440201 MS.gene054933:CDS
TAGCAGTTTCATCAAGGAAT+TGG 0.311012 8.4:-77439768 MS.gene054933:CDS
CAAGCCTCTCGTCGAAATTA+TGG 0.312035 8.4:+77440475 None:intergenic
AGCAATGAAGGTACAGAATA+TGG 0.327499 8.4:-77439935 MS.gene054933:CDS
GTTAAACAATATGAAGAGTT+AGG 0.347136 8.4:-77440351 MS.gene054933:CDS
ATATTTGAAAACAACAGATA+TGG 0.357754 8.4:+77439988 None:intergenic
TTTGACATTGTCAACTGATA+AGG 0.368653 8.4:-77440076 MS.gene054933:CDS
TGCAAAATGTTGAAGACAAA+TGG 0.380077 8.4:-77440701 MS.gene054933:CDS
TTCATTGCTAGAAGCACTCT+TGG 0.407140 8.4:+77439949 None:intergenic
GCGCAATGCGGATCCTTCTC+AGG 0.407457 8.4:-77440598 MS.gene054933:CDS
TATGTCATTGTTTGAGTCAA+AGG 0.408420 8.4:-77440445 MS.gene054933:CDS
TTGTAAAGATTATCAATTGT+AGG 0.408436 8.4:-77440524 MS.gene054933:CDS
CATCAGCAATTTCCTTATCA+TGG 0.411377 8.4:+77439833 None:intergenic
TTGTCGGATGATGAGATATT+CGG 0.417333 8.4:-77440123 MS.gene054933:CDS
CGTGGAAACAATTCGCGAAA+AGG 0.422845 8.4:-77440169 MS.gene054933:CDS
AGCTGGGACTTTCGTCGAAT+AGG 0.432888 8.4:+77440740 None:intergenic
CCTCAATGCTCTAAGTATTG+AGG 0.451275 8.4:+77439894 None:intergenic
CTCAATGCTCTAAGTATTGA+GGG 0.456627 8.4:+77439895 None:intergenic
TTCCTTTGACGATGAGAAGA+TGG 0.459653 8.4:-77440268 MS.gene054933:CDS
ATGGAATATATAAGTAGGAC+TGG 0.464288 8.4:-77440249 MS.gene054933:CDS
AAGAGTTAGGTATACCGAAA+AGG 0.464523 8.4:-77440338 MS.gene054933:CDS
GTCAAAGGAAATGCTTCATA+AGG 0.473131 8.4:-77440430 MS.gene054933:CDS
GATCCGCATTGCGCAAAGAC+GGG 0.492040 8.4:+77440607 None:intergenic
GGGTTGTGGTGATGACGATT+TGG 0.493364 8.4:-77440649 MS.gene054933:CDS
ATATAAAAGTAGTTCAGAAA+GGG 0.499107 8.4:+77439731 None:intergenic
AGAGTTAGGTATACCGAAAA+GGG 0.502937 8.4:-77440337 MS.gene054933:CDS
TTCAAAATTGTACAAATATG+TGG 0.504006 8.4:-77440214 MS.gene054933:CDS
GTTTGTCAGATGCCATGATA+AGG 0.508257 8.4:-77439845 MS.gene054933:CDS
AGGTATACCGAAAAGGGACT+TGG 0.508376 8.4:-77440331 MS.gene054933:CDS
TATTTGAAAACAACAGATAT+GGG 0.512551 8.4:+77439989 None:intergenic
AATATAAAAGTAGTTCAGAA+AGG 0.519070 8.4:+77439730 None:intergenic
GGATCCGCATTGCGCAAAGA+CGG 0.525836 8.4:+77440606 None:intergenic
AGAGATTAGCAGTTTCATCA+AGG 0.527319 8.4:-77439774 MS.gene054933:CDS
AAGAGTGCTTCTAGCAATGA+AGG 0.527541 8.4:-77439947 MS.gene054933:CDS
CAATGAAGGGTTTCTTGCAA+TGG 0.534493 8.4:+77440407 None:intergenic
AGAAGATGGAATATATAAGT+AGG 0.535407 8.4:-77440254 MS.gene054933:CDS
TTCCATCTTCTCATCGTCAA+AGG 0.562047 8.4:+77440266 None:intergenic
AAGTAGGACTGGGCTTTCCA+AGG 0.567180 8.4:-77440238 MS.gene054933:CDS
TCAAGGAATTGGACTACTAG+AGG 0.573509 8.4:-77439757 MS.gene054933:CDS
CATTGAGGATGTCCGAGGAG+AGG 0.582695 8.4:-77439879 MS.gene054933:CDS
ACTTTCGTCGAATAGGTGGC+AGG 0.582772 8.4:+77440747 None:intergenic
ATTAATAGGCATCTCTCGCG+TGG 0.592649 8.4:-77440187 MS.gene054933:CDS
TGTCAACTGATAAGGTTCAA+AGG 0.601835 8.4:-77440068 MS.gene054933:CDS
GAAAGTCCCAGCTCAAAATG+AGG 0.604863 8.4:-77440730 MS.gene054933:CDS
CCTCAATACTTAGAGCATTG+AGG 0.607754 8.4:-77439894 MS.gene054933:CDS
TGGAATATATAAGTAGGACT+GGG 0.608434 8.4:-77440248 MS.gene054933:CDS
TGGGACTTTCGTCGAATAGG+TGG 0.610226 8.4:+77440743 None:intergenic
TTAACCATAATTTCGACGAG+AGG 0.625796 8.4:-77440479 MS.gene054933:CDS
AGTTTCGACTGAACCTGAGA+AGG 0.646506 8.4:+77440585 None:intergenic
AAATGTTGAAGACAAATGGA+AGG 0.655802 8.4:-77440697 MS.gene054933:CDS
GAAGTTCTTGAAATAACCGT+CGG 0.665623 8.4:+77440288 None:intergenic
TAGAGCATTGAGGATGTCCG+AGG 0.681763 8.4:-77439884 MS.gene054933:CDS
TTGCCCGTCTTTGCGCAATG+CGG 0.689638 8.4:-77440610 MS.gene054933:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! AGTTAATGGAATTTTATAAA+AGG - chr8.4:77440684-77440703 MS.gene054933:CDS 15.0%
!! ATATTTGAAAACAACAGATA+TGG + chr8.4:77440509-77440528 None:intergenic 20.0%
!! TATTTGAAAACAACAGATAT+GGG + chr8.4:77440508-77440527 None:intergenic 20.0%
!! TTCAAAATTGTACAAATATG+TGG - chr8.4:77440280-77440299 MS.gene054933:CDS 20.0%
!! TTGTAAAGATTATCAATTGT+AGG - chr8.4:77439970-77439989 MS.gene054933:CDS 20.0%
!!! ATATCTGTTGTTTTCAAATA+TGG - chr8.4:77440508-77440527 MS.gene054933:CDS 20.0%
!!! ATTTTATAAAAGGACAAAAC+AGG - chr8.4:77440694-77440713 MS.gene054933:CDS 20.0%
! AAATATGTGGTGACATTAAT+AGG - chr8.4:77440293-77440312 MS.gene054933:CDS 25.0%
! AGAAGATGGAATATATAAGT+AGG - chr8.4:77440240-77440259 MS.gene054933:CDS 25.0%
! GTTAAACAATATGAAGAGTT+AGG - chr8.4:77440143-77440162 MS.gene054933:CDS 25.0%
! GTTGACAATGTCAAAATATT+AGG + chr8.4:77440413-77440432 None:intergenic 25.0%
!! GTGTTGAATTTTACAAAGTA+TGG - chr8.4:77440347-77440366 MS.gene054933:CDS 25.0%
!! TTTGTACAATTTTGAATCCT+TGG + chr8.4:77440276-77440295 None:intergenic 25.0%
!!! TACTGAAGTTTTGAGTAAAT+GGG - chr8.4:77439824-77439843 MS.gene054933:CDS 25.0%
!!! TTTTACAAAGTATGGTTTGT+CGG - chr8.4:77440355-77440374 MS.gene054933:CDS 25.0%
AAATGTTGAAGACAAATGGA+AGG - chr8.4:77439797-77439816 MS.gene054933:CDS 30.0%
ATGGAATATATAAGTAGGAC+TGG - chr8.4:77440245-77440264 MS.gene054933:CDS 30.0%
TATGTCATTGTTTGAGTCAA+AGG - chr8.4:77440049-77440068 MS.gene054933:CDS 30.0%
TGCAAAATGTTGAAGACAAA+TGG - chr8.4:77439793-77439812 MS.gene054933:CDS 30.0%
TGGAATATATAAGTAGGACT+GGG - chr8.4:77440246-77440265 MS.gene054933:CDS 30.0%
TTTGACATTGTCAACTGATA+AGG - chr8.4:77440418-77440437 MS.gene054933:CDS 30.0%
! AGGAACATGACTTTCATTTT+AGG - chr8.4:77440446-77440465 MS.gene054933:CDS 30.0%
! ATGAGATATTCGGTCTTTTT+GGG - chr8.4:77440381-77440400 MS.gene054933:CDS 30.0%
! TATTTTCACACAGCAATGAA+GGG + chr8.4:77440103-77440122 None:intergenic 30.0%
! TGGTTCAAATGATGATTTTG+CGG - chr8.4:77440183-77440202 MS.gene054933:CDS 30.0%
! TTATTTTCACACAGCAATGA+AGG + chr8.4:77440104-77440123 None:intergenic 30.0%
!!! ACTGAAGTTTTGAGTAAATG+GGG - chr8.4:77439825-77439844 MS.gene054933:CDS 30.0%
!!! ATTGAGGGTGTTTTCATATT+AGG + chr8.4:77440587-77440606 None:intergenic 30.0%
!!! CTACTGAAGTTTTGAGTAAA+TGG - chr8.4:77439823-77439842 MS.gene054933:CDS 30.0%
AAGAGTTAGGTATACCGAAA+AGG - chr8.4:77440156-77440175 MS.gene054933:CDS 35.0%
AGAGATTAGCAGTTTCATCA+AGG - chr8.4:77440720-77440739 MS.gene054933:CDS 35.0%
AGAGTTAGGTATACCGAAAA+GGG - chr8.4:77440157-77440176 MS.gene054933:CDS 35.0%
CATCAGCAATTTCCTTATCA+TGG + chr8.4:77440664-77440683 None:intergenic 35.0%
GAAGTTCTTGAAATAACCGT+CGG + chr8.4:77440209-77440228 None:intergenic 35.0%
GGAAATTGCTGATGAGTTAA+TGG - chr8.4:77440670-77440689 MS.gene054933:CDS 35.0%
GTCAAAGGAAATGCTTCATA+AGG - chr8.4:77440064-77440083 MS.gene054933:CDS 35.0%
TAGCAGTTTCATCAAGGAAT+TGG - chr8.4:77440726-77440745 MS.gene054933:CDS 35.0%
TGTCAACTGATAAGGTTCAA+AGG - chr8.4:77440426-77440445 MS.gene054933:CDS 35.0%
TTAACCATAATTTCGACGAG+AGG - chr8.4:77440015-77440034 MS.gene054933:CDS 35.0%
TTGTCGGATGATGAGATATT+CGG - chr8.4:77440371-77440390 MS.gene054933:CDS 35.0%
! AGCAATGAAGGTACAGAATA+TGG - chr8.4:77440559-77440578 MS.gene054933:CDS 35.0%
! ATTTCAACCTCATTTTGAGC+TGG + chr8.4:77439774-77439793 None:intergenic 35.0%
! ATTTGAACCAAGTCCCTTTT+CGG + chr8.4:77440173-77440192 None:intergenic 35.0%
! GATGAGATATTCGGTCTTTT+TGG - chr8.4:77440380-77440399 MS.gene054933:CDS 35.0%
! TTGCTTAGTGATTTGGGTTT+AGG - chr8.4:77439936-77439955 MS.gene054933:CDS 35.0%
! TTTCAACCTCATTTTGAGCT+GGG + chr8.4:77439773-77439792 None:intergenic 35.0%
!! CTCAATGCTCTAAGTATTGA+GGG + chr8.4:77440602-77440621 None:intergenic 35.0%
ACTTCGCTTGCTTAGTGATT+TGG - chr8.4:77439929-77439948 MS.gene054933:CDS 40.0%
CAATGAAGGGTTTCTTGCAA+TGG + chr8.4:77440090-77440109 None:intergenic 40.0%
CGTATTGAAAAACCTCTCCT+CGG + chr8.4:77440630-77440649 None:intergenic 40.0%
CTTCGCTTGCTTAGTGATTT+GGG - chr8.4:77439930-77439949 MS.gene054933:CDS 40.0%
GTTTGTCAGATGCCATGATA+AGG - chr8.4:77440649-77440668 MS.gene054933:CDS 40.0%
TCAAGGAATTGGACTACTAG+AGG - chr8.4:77440737-77440756 MS.gene054933:CDS 40.0%
TTCCATCTTCTCATCGTCAA+AGG + chr8.4:77440231-77440250 None:intergenic 40.0%
TTCCTTTGACGATGAGAAGA+TGG - chr8.4:77440226-77440245 MS.gene054933:CDS 40.0%
! ATTGTAGGCCTCGATTTTTC+AGG - chr8.4:77439985-77440004 MS.gene054933:CDS 40.0%
! CCTCAATGCTCTAAGTATTG+AGG + chr8.4:77440603-77440622 None:intergenic 40.0%
!! AAGAGTGCTTCTAGCAATGA+AGG - chr8.4:77440547-77440566 MS.gene054933:CDS 40.0%
!! CCTCAATACTTAGAGCATTG+AGG - chr8.4:77440600-77440619 MS.gene054933:CDS 40.0%
!! GTTTTGAGTAAATGGGGTTG+TGG - chr8.4:77439831-77439850 MS.gene054933:CDS 40.0%
!! TTCATTGCTAGAAGCACTCT+TGG + chr8.4:77440548-77440567 None:intergenic 40.0%
AGGTATACCGAAAAGGGACT+TGG - chr8.4:77440163-77440182 MS.gene054933:CDS 45.0%
AGTCGAGTCCTGAAAAATCG+AGG + chr8.4:77439996-77440015 None:intergenic 45.0%
AGTTTCGACTGAACCTGAGA+AGG + chr8.4:77439912-77439931 None:intergenic 45.0%
ATTAATAGGCATCTCTCGCG+TGG - chr8.4:77440307-77440326 MS.gene054933:CDS 45.0%
CAAGCCTCTCGTCGAAATTA+TGG + chr8.4:77440022-77440041 None:intergenic 45.0%
CGTGGAAACAATTCGCGAAA+AGG - chr8.4:77440325-77440344 MS.gene054933:CDS 45.0%
GAAAGTCCCAGCTCAAAATG+AGG - chr8.4:77439764-77439783 MS.gene054933:CDS 45.0%
! AATGATGATTTTGCGGCCGA+CGG - chr8.4:77440190-77440209 MS.gene054933:CDS 45.0%
AAGTAGGACTGGGCTTTCCA+AGG - chr8.4:77440256-77440275 MS.gene054933:CDS 50.0%
ACTTTCGTCGAATAGGTGGC+AGG + chr8.4:77439750-77439769 None:intergenic 50.0%
AGCTGGGACTTTCGTCGAAT+AGG + chr8.4:77439757-77439776 None:intergenic 50.0%
TGGGACTTTCGTCGAATAGG+TGG + chr8.4:77439754-77439773 None:intergenic 50.0%
! GGGTTGTGGTGATGACGATT+TGG - chr8.4:77439845-77439864 MS.gene054933:CDS 50.0%
!! TAGAGCATTGAGGATGTCCG+AGG - chr8.4:77440610-77440629 MS.gene054933:CDS 50.0%
CATTGAGGATGTCCGAGGAG+AGG - chr8.4:77440615-77440634 MS.gene054933:CDS 55.0%
GATCCGCATTGCGCAAAGAC+GGG + chr8.4:77439890-77439909 None:intergenic 55.0%
GGATCCGCATTGCGCAAAGA+CGG + chr8.4:77439891-77439910 None:intergenic 55.0%
TTGCCCGTCTTTGCGCAATG+CGG - chr8.4:77439884-77439903 MS.gene054933:CDS 55.0%
GCGCAATGCGGATCCTTCTC+AGG - chr8.4:77439896-77439915 MS.gene054933:CDS 60.0%


Chromosome Type Strat End Strand Name
chr8.4 gene 77439744 77440772 77439744 ID=MS.gene054933
chr8.4 mRNA 77439744 77440772 77439744 ID=MS.gene054933.t1;Parent=MS.gene054933
chr8.4 exon 77439744 77440772 77439744 ID=MS.gene054933.t1.exon1;Parent=MS.gene054933.t1
chr8.4 CDS 77439744 77440772 77439744 ID=cds.MS.gene054933.t1;Parent=MS.gene054933.t1
Gene Sequence

>MS.gene054933

ATGCCTGCCACCTATTCGACGAAAGTCCCAGCTCAAAATGAGGTTGAAATGCAAAATGTTGAAGACAAATGGAAGGATGCTACTGAAGTTTTGAGTAAATGGGGTTGTGGTGATGACGATTTGGCAAGAATATTCACTCGTTGCCCGTCTTTGCGCAATGCGGATCCTTCTCAGGTTCAGTCGAAACTTCGCTTGCTTAGTGATTTGGGTTTAGGCTCAGCTGAGCTTGTAAAGATTATCAATTGTAGGCCTCGATTTTTCAGGACTCGACTTAACCATAATTTCGACGAGAGGCTTGACTCTCTTATGTCATTGTTTGAGTCAAAGGAAATGCTTCATAAGGCCATTGCAAGAAACCCTTCATTGCTGTGTGAAAATAATTATGACATTGAACGTATTGTTAAACAATATGAAGAGTTAGGTATACCGAAAAGGGACTTGGTTCAAATGATGATTTTGCGGCCGACGGTTATTTCAAGAACTTCCTTTGACGATGAGAAGATGGAATATATAAGTAGGACTGGGCTTTCCAAGGATTCAAAATTGTACAAATATGTGGTGACATTAATAGGCATCTCTCGCGTGGAAACAATTCGCGAAAAGGTGTTGAATTTTACAAAGTATGGTTTGTCGGATGATGAGATATTCGGTCTTTTTGGGAAGTCTCCTAATATTTTGACATTGTCAACTGATAAGGTTCAAAGGAACATGACTTTCATTTTAGGCACAATGAAGCTTGAAGCTAACATAATCTTTACGTACCCATATCTGTTGTTTTCAAATATGGAGACTGTTTTGAAGCCAAGAGTGCTTCTAGCAATGAAGGTACAGAATATGGTTCCTAATATGAAAACACCCTCAATACTTAGAGCATTGAGGATGTCCGAGGAGAGGTTTTTCAATACGTTTGTCAGATGCCATGATAAGGAAATTGCTGATGAGTTAATGGAATTTTATAAAAGGACAAAACAGGTTAAGAGATTAGCAGTTTCATCAAGGAATTGGACTACTAGAGGATTCCCTTTCTGA
Protein sequence

>MS.gene054933.t1

MPATYSTKVPAQNEVEMQNVEDKWKDATEVLSKWGCGDDDLARIFTRCPSLRNADPSQVQSKLRLLSDLGLGSAELVKIINCRPRFFRTRLNHNFDERLDSLMSLFESKEMLHKAIARNPSLLCENNYDIERIVKQYEELGIPKRDLVQMMILRPTVISRTSFDDEKMEYISRTGLSKDSKLYKYVVTLIGISRVETIREKVLNFTKYGLSDDEIFGLFGKSPNILTLSTDKVQRNMTFILGTMKLEANIIFTYPYLLFSNMETVLKPRVLLAMKVQNMVPNMKTPSILRALRMSEERFFNTFVRCHDKEIADELMEFYKRTKQVKRLAVSSRNWTTRGFPF