AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene052827

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene052827.t1 MTR_6g061070 70.130 231 30 2 1 193 241 470 4.45e-110 323
MS.gene052827.t1 MTR_1g035520 71.756 131 35 1 65 193 253 383 2.83e-60 192
MS.gene052827.t1 MTR_1g035540 60.000 115 33 3 5 119 2 103 7.23e-40 132
MS.gene052827.t1 MTR_1g035570 42.188 192 105 4 2 193 209 394 1.22e-39 139
MS.gene052827.t1 MTR_1g035490 38.991 218 100 10 2 193 118 328 1.26e-37 132
MS.gene052827.t1 MTR_1g035620 33.953 215 117 4 1 192 196 408 8.69e-27 105
MS.gene052827.t1 MTR_1g035640 48.913 92 45 2 2 93 202 291 2.55e-19 85.1
MS.gene052827.t1 MTR_1g050845 31.111 180 102 3 1 158 184 363 8.37e-18 80.9
MS.gene052827.t1 MTR_5g044670 35.294 102 65 1 2 103 224 324 1.59e-12 65.1
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 37 sgRNAs with CRISPR-Local

Find 62 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GGGCATGGTTCCTTTGTGGC+TGG 0.277429 1.2:-19921644 None:intergenic
TTGAATTTGTCATGTAAATT+CGG 0.311912 1.2:-19922053 None:intergenic
TTAATACCTTGAAACTGCTT+TGG 0.331338 1.2:-19921665 None:intergenic
AAAAGACATAATATATTTAG+TGG 0.334344 1.2:+19922211 MS.gene052827:CDS
TTCCTTTGTGGCTGGGATAA+TGG 0.345212 1.2:-19921636 None:intergenic
TATAATGAACATCTCGACTA+TGG 0.355043 1.2:+19922286 MS.gene052827:CDS
CTTTGGGCATGGTTCCTTTG+TGG 0.363966 1.2:-19921648 None:intergenic
TAATACCTTGAAACTGCTTT+GGG 0.373065 1.2:-19921664 None:intergenic
TAATATATTTAGTGGAAATT+CGG 0.396970 1.2:+19922219 MS.gene052827:CDS
GGCATGGTTCCTTTGTGGCT+GGG 0.407207 1.2:-19921643 None:intergenic
AAGGAACATGACTTAAAAGT+TGG 0.442738 1.2:+19921560 MS.gene052827:CDS
GAATTTACATGACAAATTCA+AGG 0.456040 1.2:+19922055 MS.gene052827:CDS
ATTCGGTGGAGTTGAAAGTA+GGG 0.471281 1.2:+19922236 MS.gene052827:CDS
TTAGAAGTGTTGATGAGGAC+AGG 0.485676 1.2:+19921462 MS.gene052827:CDS
TGAAAGTAGGGGAAGGAACA+TGG 0.498346 1.2:+19922248 MS.gene052827:CDS
CCTTGAAACTGCTTTGGGCA+TGG 0.499094 1.2:-19921659 None:intergenic
AATTCGGTGGAGTTGAAAGT+AGG 0.502201 1.2:+19922235 MS.gene052827:CDS
AGAGATTGCAAAGTAAAGAC+TGG 0.513081 1.2:+19922340 MS.gene052827:CDS
TGTGCAAAATCATGTGTTCA+AGG 0.521657 1.2:+19922390 MS.gene052827:CDS
ATGGTAATTGTGAATGAAAG+TGG 0.526717 1.2:-19921617 None:intergenic
CCATGCCCAAAGCAGTTTCA+AGG 0.526984 1.2:+19921659 MS.gene052827:CDS
GACTATGGATGGTTCACTAA+AGG 0.536976 1.2:+19922301 MS.gene052827:CDS
TACATGAATGAGTTATTGCA+AGG 0.543984 1.2:+19921428 MS.gene052827:CDS
TATATTTAGTGGAAATTCGG+TGG 0.544355 1.2:+19922222 MS.gene052827:CDS
TATTCGTTTGAAAACCATGT+AGG 0.557476 1.2:-19921407 None:intergenic
ATGGATGGTTCACTAAAGGC+TGG 0.558556 1.2:+19922305 MS.gene052827:CDS
ATGAACATCTCGACTATGGA+TGG 0.566956 1.2:+19922290 MS.gene052827:CDS
TGAAACAGAGGCTACCTACA+TGG 0.580260 1.2:+19921393 None:intergenic
AACAATTAGAAGTGTTGATG+AGG 0.583313 1.2:+19921457 MS.gene052827:CDS
GGAAGGAACATGGTTTGTAG+AGG 0.629163 1.2:+19922258 MS.gene052827:CDS
TTCGGTGGAGTTGAAAGTAG+GGG 0.634551 1.2:+19922237 MS.gene052827:CDS
GAATGAGTTATTGCAAGGGA+AGG 0.643476 1.2:+19921433 MS.gene052827:CDS
GTGGAGTTGAAAGTAGGGGA+AGG 0.644645 1.2:+19922241 MS.gene052827:CDS
TAGAAGTGTTGATGAGGACA+GGG 0.646868 1.2:+19921463 MS.gene052827:CDS
TACCATTATCCCAGCCACAA+AGG 0.660933 1.2:+19921634 MS.gene052827:CDS
ACATGAATGAGTTATTGCAA+GGG 0.661417 1.2:+19921429 MS.gene052827:CDS
GTGTTGATGAGGACAGGGCA+CGG 0.684939 1.2:+19921468 MS.gene052827:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAAAGACATAATATATTTAG+TGG + chr1.2:19922211-19922230 MS.gene052827:CDS 15.0%
!! CTTGAAAAATAAAATTAAGA+TGG - chr1.2:19921958-19921977 None:intergenic 15.0%
!! TAATATATTTAGTGGAAATT+CGG + chr1.2:19922219-19922238 MS.gene052827:CDS 15.0%
!! TTGAATTTGTCATGTAAATT+CGG - chr1.2:19922056-19922075 None:intergenic 20.0%
! AGAACAAAGAAAACAGTTTA+AGG - chr1.2:19922010-19922029 None:intergenic 25.0%
! AGTAGTATGTTTACATTACA+TGG - chr1.2:19921779-19921798 None:intergenic 25.0%
! GAATTTACATGACAAATTCA+AGG + chr1.2:19922055-19922074 MS.gene052827:CDS 25.0%
! TTTGTTCTTATATATGCAGT+TGG + chr1.2:19922165-19922184 MS.gene052827:intron 25.0%
AAGGAACATGACTTAAAAGT+TGG + chr1.2:19921560-19921579 MS.gene052827:CDS 30.0%
ACATATTCCATATCTTCTTC+GGG - chr1.2:19921875-19921894 None:intergenic 30.0%
ACATGAATGAGTTATTGCAA+GGG + chr1.2:19921429-19921448 MS.gene052827:CDS 30.0%
ATGGTAATTGTGAATGAAAG+TGG - chr1.2:19921620-19921639 None:intergenic 30.0%
CACATATTCCATATCTTCTT+CGG - chr1.2:19921876-19921895 None:intergenic 30.0%
GAAGAAGATATGGAATATGT+GGG + chr1.2:19921875-19921894 MS.gene052827:intron 30.0%
TAATACCTTGAAACTGCTTT+GGG - chr1.2:19921667-19921686 None:intergenic 30.0%
TACATGAATGAGTTATTGCA+AGG + chr1.2:19921428-19921447 MS.gene052827:CDS 30.0%
TATAATGAACATCTCGACTA+TGG + chr1.2:19922286-19922305 MS.gene052827:CDS 30.0%
TATATTTAGTGGAAATTCGG+TGG + chr1.2:19922222-19922241 MS.gene052827:CDS 30.0%
TATTCGTTTGAAAACCATGT+AGG - chr1.2:19921410-19921429 None:intergenic 30.0%
TCAAGGTTTCAATTGTTTGA+AGG + chr1.2:19922407-19922426 MS.gene052827:CDS 30.0%
TTAATACCTTGAAACTGCTT+TGG - chr1.2:19921668-19921687 None:intergenic 30.0%
! TTTTGTGACATCATTAGACA+AGG + chr1.2:19922079-19922098 MS.gene052827:CDS 30.0%
!! AACAATTAGAAGTGTTGATG+AGG + chr1.2:19921457-19921476 MS.gene052827:CDS 30.0%
!! CTGATTTTATTTGCACTTGT+TGG - chr1.2:19921844-19921863 None:intergenic 30.0%
!!! CAATGACAGTTTTTTAATGC+AGG + chr1.2:19921517-19921536 MS.gene052827:CDS 30.0%
AGAGATTGCAAAGTAAAGAC+TGG + chr1.2:19922340-19922359 MS.gene052827:CDS 35.0%
CGAAGAAGATATGGAATATG+TGG + chr1.2:19921874-19921893 MS.gene052827:intron 35.0%
TGTGCAAAATCATGTGTTCA+AGG + chr1.2:19922390-19922409 MS.gene052827:CDS 35.0%
! ATGGAATATGTGGGCAATTT+TGG + chr1.2:19921884-19921903 MS.gene052827:intron 35.0%
! TGTCTTTTTAACAGCTCACT+TGG - chr1.2:19922199-19922218 None:intergenic 35.0%
!! TGGTTGGAAGTCATTTTCAA+AGG + chr1.2:19921541-19921560 MS.gene052827:CDS 35.0%
!!! GACAGTTTTTTAATGCAGGT+TGG + chr1.2:19921521-19921540 MS.gene052827:CDS 35.0%
!!! GTTTTTTAATGCAGGTTGGT+TGG + chr1.2:19921525-19921544 MS.gene052827:CDS 35.0%
AACAGCTGCCTTAAAACACA+AGG + chr1.2:19921920-19921939 MS.gene052827:intron 40.0%
ATGAACATCTCGACTATGGA+TGG + chr1.2:19922290-19922309 MS.gene052827:CDS 40.0%
GAATGAGTTATTGCAAGGGA+AGG + chr1.2:19921433-19921452 MS.gene052827:CDS 40.0%
GACTATGGATGGTTCACTAA+AGG + chr1.2:19922301-19922320 MS.gene052827:CDS 40.0%
! AATTCGGTGGAGTTGAAAGT+AGG + chr1.2:19922235-19922254 MS.gene052827:CDS 40.0%
! ATTCGGTGGAGTTGAAAGTA+GGG + chr1.2:19922236-19922255 MS.gene052827:CDS 40.0%
! TCCTGAGACCTTGTGTTTTA+AGG - chr1.2:19921931-19921950 None:intergenic 40.0%
!! TAGAAGTGTTGATGAGGACA+GGG + chr1.2:19921463-19921482 MS.gene052827:CDS 40.0%
!! TTAGAAGTGTTGATGAGGAC+AGG + chr1.2:19921462-19921481 MS.gene052827:CDS 40.0%
ATGGATGGTTCACTAAAGGC+TGG + chr1.2:19922305-19922324 MS.gene052827:CDS 45.0%
GACAATGCCCGAAGAAGATA+TGG + chr1.2:19921865-19921884 MS.gene052827:intron 45.0%
GCCTTAAAACACAAGGTCTC+AGG + chr1.2:19921927-19921946 MS.gene052827:intron 45.0%
TACCATTATCCCAGCCACAA+AGG + chr1.2:19921634-19921653 MS.gene052827:CDS 45.0%
TGAAAGTAGGGGAAGGAACA+TGG + chr1.2:19922248-19922267 MS.gene052827:CDS 45.0%
TTCCTTTGTGGCTGGGATAA+TGG - chr1.2:19921639-19921658 None:intergenic 45.0%
TTCGGTGGAGTTGAAAGTAG+GGG + chr1.2:19922237-19922256 MS.gene052827:CDS 45.0%
! GGAAGGAACATGGTTTGTAG+AGG + chr1.2:19922258-19922277 MS.gene052827:CDS 45.0%
!!! TATTAATTTCATTATTATTT+TGG + chr1.2:19921682-19921701 MS.gene052827:intron 5.0%
CCATGCCCAAAGCAGTTTCA+AGG + chr1.2:19921659-19921678 MS.gene052827:CDS 50.0%
CTTTGGGCATGGTTCCTTTG+TGG - chr1.2:19921651-19921670 None:intergenic 50.0%
GTGGAGTTGAAAGTAGGGGA+AGG + chr1.2:19922241-19922260 MS.gene052827:CDS 50.0%
! CCTTGAAACTGCTTTGGGCA+TGG - chr1.2:19921662-19921681 None:intergenic 50.0%
!! TCTGCTTTTGATCCCCGACA+AGG + chr1.2:19921800-19921819 MS.gene052827:intron 50.0%
CTGCATGTCGACGACCTTGT+CGG - chr1.2:19921817-19921836 None:intergenic 55.0%
GGCATGGTTCCTTTGTGGCT+GGG - chr1.2:19921646-19921665 None:intergenic 55.0%
TGCATGTCGACGACCTTGTC+GGG - chr1.2:19921816-19921835 None:intergenic 55.0%
! GTGTTGATGAGGACAGGGCA+CGG + chr1.2:19921468-19921487 MS.gene052827:CDS 55.0%
GCATGTCGACGACCTTGTCG+GGG - chr1.2:19921815-19921834 None:intergenic 60.0%
GGGCATGGTTCCTTTGTGGC+TGG - chr1.2:19921647-19921666 None:intergenic 60.0%


Chromosome Type Strat End Strand Name
chr1.2 gene 19921401 19922426 19921401 ID=MS.gene052827
chr1.2 mRNA 19921401 19922426 19921401 ID=MS.gene052827.t1;Parent=MS.gene052827
chr1.2 exon 19921401 19921680 19921401 ID=MS.gene052827.t1.exon1;Parent=MS.gene052827.t1
chr1.2 CDS 19921401 19921680 19921401 ID=cds.MS.gene052827.t1;Parent=MS.gene052827.t1
chr1.2 exon 19922042 19922100 19922042 ID=MS.gene052827.t1.exon2;Parent=MS.gene052827.t1
chr1.2 CDS 19922042 19922100 19922042 ID=cds.MS.gene052827.t1;Parent=MS.gene052827.t1
chr1.2 exon 19922184 19922426 19922184 ID=MS.gene052827.t1.exon3;Parent=MS.gene052827.t1
chr1.2 CDS 19922184 19922426 19922184 ID=cds.MS.gene052827.t1;Parent=MS.gene052827.t1
Gene Sequence

>MS.gene052827

AGGCTACCTACATGGTTTTCAAACGAATACATGAATGAGTTATTGCAAGGGAAGGCAACAATTAGAAGTGTTGATGAGGACAGGGCACGGTACGTGACGTTAAACTTTGATAAAAGCAATGACAGTTTTTTAATGCAGGTTGGTTGGAAGTCATTTTCAAAGGAACATGACTTAAAAGTTGGTGATGCATGTAAATTTGAGATGACTCAACGCGAACCACTTTCATTCACAATTACCATTATCCCAGCCACAAAGGAACCATGCCCAAAGCAGTTTCAAGGTATTAATTTCATTATTATTTTGGAAGAAACACATTTTAACATAGTTTAATTTCAATATATATATATATATATATATATATATATATATATATGTCCATGTAATGTAAACATACTACTCTCTGCTTTTGATCCCCGACAAGGTCGTCGACATGCAGAAAACCAACAAGTGCAAATAAAATCAGAGACAATGCCCGAAGAAGATATGGAATATGTGGGCAATTTTGGAGAACAAATTTCAAACAGCTGCCTTAAAACACAAGGTCTCAGGAGTATCCATCTTAATTTTATTTTTCAAGCTTTTATTGTGTAAAATTCATGAAAATATCCTTAAACTGTTTTCTTTGTTCTTCATTACTGCAGATTCTGTAAGTCCGAATTTACATGACAAATTCAAGGTTTTTGTGACATCATTAGACAAGGTATGAATTACTTAAAATGTTATTACATTGTATATAACTGTGTTGTGAATGTAATTTTTTTTAATTTGTTCTTATATATGCAGTTGGTTGTACTACCAAGTGAGCTGTTAAAAAGACATAATATATTTAGTGGAAATTCGGTGGAGTTGAAAGTAGGGGAAGGAACATGGTTTGTAGAGGTGAGTTATAATGAACATCTCGACTATGGATGGTTCACTAAAGGCTGGCAAGAGTTTCTGAGAGATTGCAAAGTAAAGACTGGAGACACTTGCTTGTTTGAGATGATTGATGTGCAAAATCATGTGTTCAAGGTTTCAATTGTTTGA
Protein sequence

>MS.gene052827.t1

RLPTWFSNEYMNELLQGKATIRSVDEDRARYVTLNFDKSNDSFLMQVGWKSFSKEHDLKVGDACKFEMTQREPLSFTITIIPATKEPCPKQFQDSVSPNLHDKFKVFVTSLDKLVVLPSELLKRHNIFSGNSVELKVGEGTWFVEVSYNEHLDYGWFTKGWQEFLRDCKVKTGDTCLFEMIDVQNHVFKVSIV