AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene042374

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene042374.t1 MTR_5g036670 86.170 94 13 0 3 96 77 170 1.41e-47 166
MS.gene042374.t1 MTR_8g062700 71.250 80 23 0 3 82 76 155 7.45e-32 120
MS.gene042374.t1 MTR_8g062700 71.250 80 23 0 3 82 76 155 7.52e-32 120
MS.gene042374.t1 MTR_6g008970 64.773 88 31 0 3 90 97 184 1.22e-30 117
MS.gene042374.t1 MTR_6g008995 63.636 88 30 2 3 90 14 99 2.85e-27 106
MS.gene042374.t1 MTR_6g008995 63.636 88 30 2 3 90 71 156 4.46e-27 106
MS.gene042374.t1 MTR_1g023820 100.000 36 0 0 3 38 21 56 3.33e-19 79.3
MS.gene042374.t1 MTR_7g013410 41.935 93 43 3 3 92 32 116 9.87e-16 70.5
MS.gene042374.t1 MTR_8g062350 32.374 139 52 4 8 107 53 188 1.14e-13 66.6
MS.gene042374.t1 MTR_1g105955 44.872 78 36 2 1 78 48 118 1.18e-12 63.5
MS.gene042374.t1 MTR_0091s0080 34.066 91 56 2 89 179 387 473 4.33e-12 63.9
MS.gene042374.t1 MTR_1g105960 56.818 44 19 0 3 46 35 78 5.65e-12 60.1
MS.gene042374.t1 MTR_4g133300 36.905 84 47 1 3 86 43 120 3.57e-11 60.5
MS.gene042374.t1 MTR_4g133470 38.750 80 43 1 3 82 43 116 3.91e-11 60.5
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene042374.t1 AT1G70060 70.787 89 25 1 3 90 48 136 3.57e-34 127
MS.gene042374.t1 AT1G70060 70.787 89 25 1 3 90 48 136 3.57e-34 127
MS.gene042374.t1 AT1G24190 71.591 88 25 0 3 90 48 135 9.96e-34 126
MS.gene042374.t1 AT1G24190 71.591 88 25 0 3 90 48 135 1.02e-33 126
MS.gene042374.t1 AT1G24190 71.591 88 25 0 3 90 48 135 1.06e-33 126
MS.gene042374.t1 AT3G01320 60.000 90 35 1 3 92 91 179 1.02e-26 106
MS.gene042374.t1 AT5G15020 62.791 86 30 1 4 89 87 170 1.05e-26 106
MS.gene042374.t1 AT5G15020 62.791 86 30 1 4 89 87 170 1.05e-26 106
MS.gene042374.t1 AT3G01320 60.000 90 35 1 3 92 91 179 1.05e-26 106
MS.gene042374.t1 AT1G59890 59.091 88 34 1 3 90 79 164 2.61e-26 105
MS.gene042374.t1 AT1G59890 59.091 88 34 1 3 90 79 164 2.77e-26 105
MS.gene042374.t1 AT1G59890 59.091 88 34 1 3 90 79 164 2.87e-26 105
MS.gene042374.t1 AT1G59890 59.091 88 34 1 3 90 79 164 2.91e-26 105
MS.gene042374.t1 AT1G10450 61.250 80 29 1 3 82 67 144 1.43e-25 103
MS.gene042374.t1 AT1G10450 61.250 80 29 1 3 82 67 144 1.43e-25 103
MS.gene042374.t1 AT1G10450 61.250 80 29 1 3 82 118 195 1.46e-25 103
MS.gene042374.t1 AT1G24200 57.500 80 31 1 3 82 48 124 3.00e-22 89.0
MS.gene042374.t1 AT1G70030 53.947 76 33 2 8 83 50 123 1.11e-17 76.3
MS.gene042374.t1 AT5G35610 35.965 114 58 3 3 105 44 153 1.98e-13 65.1
MS.gene042374.t1 AT1G70030 50.000 72 33 2 8 77 61 131 1.89e-12 62.0
MS.gene042374.t1 AT1G70030 56.140 57 24 1 8 64 61 116 3.63e-12 60.8

Find 45 sgRNAs with CRISPR-Local

Find 75 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TCATGTTTACAAGTCATTTA+TGG 0.140196 6.2:-80270136 MS.gene042374:CDS
CTCATGGCCCTTTGGCAAAA+AGG 0.248205 6.2:+80270368 None:intergenic
CAAGAAGATCCGGGTGGTTT+TGG 0.249415 6.2:+80269933 None:intergenic
TTCATCTGTGTCGTGTTGAT+TGG 0.378078 6.2:-80269901 MS.gene042374:CDS
AAGTTAACCATTACTTTATG+AGG 0.408474 6.2:-80269699 MS.gene042374:CDS
TTGTATGAGTGCACTGCAAA+GGG 0.421632 6.2:+80269770 None:intergenic
TCGTGTTGATTGGCGGTGAC+TGG 0.441416 6.2:-80269891 MS.gene042374:CDS
GAGTTATGTGAACACGATAA+AGG 0.446913 6.2:-80270280 MS.gene042374:intron
AGGGTAATCTCATGGCCCTT+TGG 0.451315 6.2:+80270360 None:intergenic
ACTCGGCATCAGTGGGGAAG+GGG 0.451431 6.2:-80269821 MS.gene042374:CDS
ACTGCAAAGGGGTATGTCTC+AGG 0.456330 6.2:+80269782 None:intergenic
AACCACCCGGATCTTCTTGA+AGG 0.457397 6.2:-80269929 MS.gene042374:CDS
TGGTTGAGGTTGCTCATCCT+CGG 0.459938 6.2:+80270332 None:intergenic
CAGGTACTTTCCCTCTTGGT+AGG 0.460534 6.2:+80269673 None:intergenic
GGTCATAGAGACTTGATCTT+GGG 0.467943 6.2:-80270399 MS.gene042374:CDS
ACATCAGGTACTTTCCCTCT+TGG 0.471918 6.2:+80269669 None:intergenic
ATAAACCCTTCAAGAAGATC+CGG 0.477187 6.2:+80269923 None:intergenic
TTTATGCAGACTCGGTTTCA+GGG 0.487740 6.2:-80270165 MS.gene042374:intron
AAACTCGGCATCAGTGGGGA+AGG 0.492373 6.2:-80269823 MS.gene042374:CDS
CTATAAAACTCGGCATCAGT+GGG 0.502922 6.2:-80269828 MS.gene042374:CDS
AGGTACTTTCCCTCTTGGTA+GGG 0.505190 6.2:+80269674 None:intergenic
GCTATAAAACTCGGCATCAG+TGG 0.506265 6.2:-80269829 MS.gene042374:CDS
ATCTGTGTCGTGTTGATTGG+CGG 0.509936 6.2:-80269898 MS.gene042374:CDS
AGGTCATAGAGACTTGATCT+TGG 0.513611 6.2:-80270400 MS.gene042374:CDS
CTCGGCATCAGTGGGGAAGG+GGG 0.515169 6.2:-80269820 MS.gene042374:CDS
AACTCGGCATCAGTGGGGAA+GGG 0.528339 6.2:-80269822 MS.gene042374:CDS
TTGCTCATCCTCGGACGAAA+GGG 0.539598 6.2:+80270341 None:intergenic
CTTGTATGAGTGCACTGCAA+AGG 0.547650 6.2:+80269769 None:intergenic
GTTGCTCATCCTCGGACGAA+AGG 0.549267 6.2:+80270340 None:intergenic
ACCACCCGGATCTTCTTGAA+GGG 0.554045 6.2:-80269928 MS.gene042374:CDS
TATATTCATCCTTCGAGCAA+TGG 0.563072 6.2:-80269745 MS.gene042374:CDS
CGGACGAAAGGGTAATCTCA+TGG 0.581909 6.2:+80270352 None:intergenic
TGAGATTACCCTTTCGTCCG+AGG 0.584557 6.2:-80270349 MS.gene042374:CDS
TAAACCCTTCAAGAAGATCC+GGG 0.599628 6.2:+80269924 None:intergenic
TGCATTCTTCCAAAACCACC+CGG 0.599692 6.2:-80269942 MS.gene042374:CDS
GTTGGTCATGCTATAAAACT+CGG 0.605058 6.2:-80269838 MS.gene042374:CDS
TCATTGACACCATTGCTCGA+AGG 0.620805 6.2:+80269736 None:intergenic
TAGGGCACCTCATAAAGTAA+TGG 0.626853 6.2:+80269692 None:intergenic
ATTTGTAGAGTTGATACTGA+TGG 0.633224 6.2:-80270453 MS.gene042374:intron
TATGAGGTGCCCTACCAAGA+GGG 0.635144 6.2:-80269683 MS.gene042374:CDS
TTATGAGGTGCCCTACCAAG+AGG 0.660657 6.2:-80269684 MS.gene042374:CDS
TGGTGTCATTGAAAGAGTGA+AGG 0.685356 6.2:-80270433 MS.gene042374:CDS
TGTATGAGTGCACTGCAAAG+GGG 0.718580 6.2:+80269771 None:intergenic
ACCCTTCAAGAAGATCCGGG+TGG 0.747614 6.2:+80269927 None:intergenic
TATAAAACTCGGCATCAGTG+GGG 0.747744 6.2:-80269827 MS.gene042374:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! GTTGTTTTTGTATATATATT+GGG - chr6.2:80269684-80269703 MS.gene042374:CDS 15.0%
!! ATATATATACAAAAACAACG+TGG + chr6.2:80269683-80269702 None:intergenic 20.0%
!!! AATTGATTTGTTTATCCTTT+TGG - chr6.2:80269733-80269752 MS.gene042374:CDS 20.0%
!!! CGTTGTTTTTGTATATATAT+TGG - chr6.2:80269683-80269702 MS.gene042374:CDS 20.0%
!!! TAAAATTCAACCTTCTTTTT+TGG + chr6.2:80269903-80269922 None:intergenic 20.0%
! AAGTTAACCATTACTTTATG+AGG - chr6.2:80270513-80270532 MS.gene042374:intron 25.0%
! CATATTGAATACGTACAAAA+AGG - chr6.2:80270100-80270119 MS.gene042374:intron 25.0%
! TAGAATGTTTGTGAGTTTAA+TGG - chr6.2:80269956-80269975 MS.gene042374:intron 25.0%
! TCATGTTTACAAGTCATTTA+TGG - chr6.2:80270076-80270095 MS.gene042374:intron 25.0%
! TTTGTATATATATTGGGAGA+GGG - chr6.2:80269690-80269709 MS.gene042374:CDS 25.0%
!! TTTTGTATATATATTGGGAG+AGG - chr6.2:80269689-80269708 MS.gene042374:CDS 25.0%
!!! AGTTTTAGTTTTGAGCTTAA+TGG - chr6.2:80270018-80270037 MS.gene042374:intron 25.0%
! ATTTAACACCTTTTTGCCAA+AGG - chr6.2:80269836-80269855 MS.gene042374:CDS 30.0%
! TTTAACACCTTTTTGCCAAA+GGG - chr6.2:80269837-80269856 MS.gene042374:CDS 30.0%
!! ATTTGTAGAGTTGATACTGA+TGG - chr6.2:80269759-80269778 MS.gene042374:CDS 30.0%
AACTCTACAAATGCACCAAA+AGG + chr6.2:80269751-80269770 None:intergenic 35.0%
ATAAACCCTTCAAGAAGATC+CGG + chr6.2:80270292-80270311 None:intergenic 35.0%
GAGTTATGTGAACACGATAA+AGG - chr6.2:80269932-80269951 MS.gene042374:CDS 35.0%
GTCAGGAAAATCTGTAATGT+TGG - chr6.2:80270170-80270189 MS.gene042374:intron 35.0%
GTTGGTCATGCTATAAAACT+CGG - chr6.2:80270374-80270393 MS.gene042374:CDS 35.0%
TATATTCATCCTTCGAGCAA+TGG - chr6.2:80270467-80270486 MS.gene042374:intron 35.0%
! AGAGTGAAGGAACTTTTTAG+AGG - chr6.2:80269792-80269811 MS.gene042374:CDS 35.0%
!!! TCAACCTTCTTTTTTGGTTG+AGG + chr6.2:80269897-80269916 None:intergenic 35.0%
AATCATGATTGCACTTCTCC+AGG - chr6.2:80270243-80270262 MS.gene042374:intron 40.0%
ACATACCTCTTTGTAGACCA+GGG + chr6.2:80270141-80270160 None:intergenic 40.0%
AGGTCATAGAGACTTGATCT+TGG - chr6.2:80269812-80269831 MS.gene042374:CDS 40.0%
CACAGCAATATGTCAAGTAC+TGG + chr6.2:80270212-80270231 None:intergenic 40.0%
CTATAAAACTCGGCATCAGT+GGG - chr6.2:80270384-80270403 MS.gene042374:CDS 40.0%
GAAACCGAGTCTGCATAAAA+AGG + chr6.2:80270046-80270065 None:intergenic 40.0%
GCAACCTCAACCAAAAAAGA+AGG - chr6.2:80269890-80269909 MS.gene042374:CDS 40.0%
GGTCATAGAGACTTGATCTT+GGG - chr6.2:80269813-80269832 MS.gene042374:CDS 40.0%
TAAACCCTTCAAGAAGATCC+GGG + chr6.2:80270291-80270310 None:intergenic 40.0%
TATAAAACTCGGCATCAGTG+GGG - chr6.2:80270385-80270404 MS.gene042374:CDS 40.0%
TTGTATGAGTGCACTGCAAA+GGG + chr6.2:80270445-80270464 None:intergenic 40.0%
! AGGTATGTGCTGTTATAGTC+AGG - chr6.2:80270153-80270172 MS.gene042374:CDS 40.0%
! GGTTCCTTTTTATGCAGACT+CGG - chr6.2:80270039-80270058 MS.gene042374:intron 40.0%
! GTGTTGCGTAATTTTCGTGT+TGG - chr6.2:80270356-80270375 MS.gene042374:CDS 40.0%
! TAGGGCACCTCATAAAGTAA+TGG + chr6.2:80270523-80270542 None:intergenic 40.0%
! TTCATCTGTGTCGTGTTGAT+TGG - chr6.2:80270311-80270330 MS.gene042374:CDS 40.0%
! TTTATGCAGACTCGGTTTCA+GGG - chr6.2:80270047-80270066 MS.gene042374:intron 40.0%
!! AGCAATATGTCAAGTACTGG+AGG + chr6.2:80270209-80270228 None:intergenic 40.0%
!! TGGTGTCATTGAAAGAGTGA+AGG - chr6.2:80269779-80269798 MS.gene042374:CDS 40.0%
!! TTTTATGCAGACTCGGTTTC+AGG - chr6.2:80270046-80270065 MS.gene042374:intron 40.0%
AGGTACTTTCCCTCTTGGTA+GGG + chr6.2:80270541-80270560 None:intergenic 45.0%
CACATACCTCTTTGTAGACC+AGG + chr6.2:80270142-80270161 None:intergenic 45.0%
CTTGTATGAGTGCACTGCAA+AGG + chr6.2:80270446-80270465 None:intergenic 45.0%
GCTATAAAACTCGGCATCAG+TGG - chr6.2:80270383-80270402 MS.gene042374:CDS 45.0%
TATCACCCTGGTCTACAAAG+AGG - chr6.2:80270133-80270152 MS.gene042374:CDS 45.0%
TCATTGACACCATTGCTCGA+AGG + chr6.2:80270479-80270498 None:intergenic 45.0%
TCTTTGTAGACCAGGGTGAT+AGG + chr6.2:80270134-80270153 None:intergenic 45.0%
TGCATTCTTCCAAAACCACC+CGG - chr6.2:80270270-80270289 MS.gene042374:intron 45.0%
TGTATGAGTGCACTGCAAAG+GGG + chr6.2:80270444-80270463 None:intergenic 45.0%
TTTGGAAGAATGCAGCAACC+TGG + chr6.2:80270264-80270283 None:intergenic 45.0%
!! ATCTGTGTCGTGTTGATTGG+CGG - chr6.2:80270314-80270333 MS.gene042374:CDS 45.0%
AACCACCCGGATCTTCTTGA+AGG - chr6.2:80270283-80270302 MS.gene042374:CDS 50.0%
ACCACCCGGATCTTCTTGAA+GGG - chr6.2:80270284-80270303 MS.gene042374:CDS 50.0%
AGGGTAATCTCATGGCCCTT+TGG + chr6.2:80269855-80269874 None:intergenic 50.0%
CAGGTACTTTCCCTCTTGGT+AGG + chr6.2:80270542-80270561 None:intergenic 50.0%
CGGACGAAAGGGTAATCTCA+TGG + chr6.2:80269863-80269882 None:intergenic 50.0%
CTCATGGCCCTTTGGCAAAA+AGG + chr6.2:80269847-80269866 None:intergenic 50.0%
GGAAAGTAAGCCTATCACCC+TGG - chr6.2:80270121-80270140 MS.gene042374:intron 50.0%
TGAGATTACCCTTTCGTCCG+AGG - chr6.2:80269863-80269882 MS.gene042374:CDS 50.0%
TGGTTGAGGTTGCTCATCCT+CGG + chr6.2:80269883-80269902 None:intergenic 50.0%
TTGCTCATCCTCGGACGAAA+GGG + chr6.2:80269874-80269893 None:intergenic 50.0%
! ACTGCAAAGGGGTATGTCTC+AGG + chr6.2:80270433-80270452 None:intergenic 50.0%
! CAAGAAGATCCGGGTGGTTT+TGG + chr6.2:80270282-80270301 None:intergenic 50.0%
! TATGAGGTGCCCTACCAAGA+GGG - chr6.2:80270529-80270548 MS.gene042374:intron 50.0%
! TTATGAGGTGCCCTACCAAG+AGG - chr6.2:80270528-80270547 MS.gene042374:intron 50.0%
AAACTCGGCATCAGTGGGGA+AGG - chr6.2:80270389-80270408 MS.gene042374:CDS 55.0%
AACTCGGCATCAGTGGGGAA+GGG - chr6.2:80270390-80270409 MS.gene042374:CDS 55.0%
ACCCTTCAAGAAGATCCGGG+TGG + chr6.2:80270288-80270307 None:intergenic 55.0%
GTTGCTCATCCTCGGACGAA+AGG + chr6.2:80269875-80269894 None:intergenic 55.0%
!! TCGTGTTGATTGGCGGTGAC+TGG - chr6.2:80270321-80270340 MS.gene042374:CDS 55.0%
ACTCGGCATCAGTGGGGAAG+GGG - chr6.2:80270391-80270410 MS.gene042374:CDS 60.0%
CTCGGCATCAGTGGGGAAGG+GGG - chr6.2:80270392-80270411 MS.gene042374:CDS 65.0%


Chromosome Type Strat End Strand Name
chr6.2 gene 80269672 80270562 80269672 ID=MS.gene042374
chr6.2 mRNA 80269672 80270562 80269672 ID=MS.gene042374.t1;Parent=MS.gene042374
chr6.2 exon 80270558 80270562 80270558 ID=MS.gene042374.t1.exon1;Parent=MS.gene042374.t1
chr6.2 CDS 80270558 80270562 80270558 ID=cds.MS.gene042374.t1;Parent=MS.gene042374.t1
chr6.2 exon 80270281 80270467 80270281 ID=MS.gene042374.t1.exon2;Parent=MS.gene042374.t1
chr6.2 CDS 80270281 80270467 80270281 ID=cds.MS.gene042374.t1;Parent=MS.gene042374.t1
chr6.2 exon 80270123 80270178 80270123 ID=MS.gene042374.t1.exon3;Parent=MS.gene042374.t1
chr6.2 CDS 80270123 80270178 80270123 ID=cds.MS.gene042374.t1;Parent=MS.gene042374.t1
chr6.2 exon 80269672 80269969 80269672 ID=MS.gene042374.t1.exon4;Parent=MS.gene042374.t1
chr6.2 CDS 80269672 80269969 80269672 ID=cds.MS.gene042374.t1;Parent=MS.gene042374.t1
Gene Sequence

>MS.gene042374

ATGTTGTACCACGTTGTTTTTGTATATATATTGGGAGAGGGATTATGAATTTGTTAGTTGTAATTGATTTGTTTATCCTTTTGGTGCATTTGTAGAGTTGATACTGATGGTGTCATTGAAAGAGTGAAGGAACTTTTTAGAGGTCATAGAGACTTGATCTTGGGATTTAACACCTTTTTGCCAAAGGGCCATGAGATTACCCTTTCGTCCGAGGATGAGCAACCTCAACCAAAAAAGAAGGTTGAATTTTATGAAGCTACGAGTTATGTGAACACGATAAAGGTTAGAATGTTTGTGAGTTTAATGGATTCTCTTCATGCAGATTTGTTTGCAATGTAGAATTAATAGTTTTAGTTTTGAGCTTAATGGTTCCTTTTTATGCAGACTCGGTTTCAGGGCGATGTTCATGTTTACAAGTCATTTATGGACATATTGAATACGTACAAAAAGGAAAGTAAGCCTATCACCCTGGTCTACAAAGAGGTATGTGCTGTTATAGTCAGGAAAATCTGTAATGTTGGTTTTTTTTTATTTCCTCCAGTACTTGACATATTGCTGTGATACACATTTTAATCATGATTGCACTTCTCCAGGTTGCTGCATTCTTCCAAAACCACCCGGATCTTCTTGAAGGGTTTATTCATCTGTGTCGTGTTGATTGGCGGTGACTGGAAAGCTATCTGTGTGTTGCGTAATTTTCGTGTTGGTCATGCTATAAAACTCGGCATCAGTGGGGAAGGGGGTGCTGATGTTGTGTACCTGAGACATACCCCTTTGCAGTGCACTCATACAAGCTATATTCATCCTTCGAGCAATGGTGTCAATGAGAAATTTGTATATCAAGTTAACCATTACTTTATGAGGTGCCCTACCAAGAGGGAAAGTACCTGA
Protein sequence

>MS.gene042374.t1

MLVDTDGVIERVKELFRGHRDLILGFNTFLPKGHEITLSSEDEQPQPKKKVEFYEATSYVNTIKTRFQGDVHVYKSFMDILNTLLHSSKTTRIFLKGLFICVVLIGGDWKAICVLRNFRVGHAIKLGISGEGGADVVYLRHTPLQCTHTSYIHPSSNGVNEKFVYQVNHYFMRCPTKREST