AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene008887

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene008887.t1 MTR_2g076780 61.957 92 35 0 23 114 21 112 1.30e-35 125
MS.gene008887.t1 MTR_8g069080 61.538 91 35 0 24 114 54 144 1.66e-34 124
MS.gene008887.t1 MTR_5g065440 48.837 86 44 0 3 88 22 107 2.04e-22 92.0
MS.gene008887.t1 MTR_5g020510 65.306 49 17 0 39 87 99 147 1.13e-21 90.5
MS.gene008887.t1 MTR_5g032600 62.903 62 20 1 36 97 75 133 2.03e-21 89.4
MS.gene008887.t1 MTR_3g100650 75.000 52 13 0 37 88 78 129 3.48e-21 89.0
MS.gene008887.t1 MTR_1g077020 67.308 52 17 0 37 88 7 58 5.52e-21 86.7
MS.gene008887.t1 MTR_4g134580 55.172 58 26 0 39 96 113 170 5.37e-19 84.3
MS.gene008887.t1 MTR_3g039810 51.471 68 30 2 37 102 18 84 2.87e-17 73.9
MS.gene008887.t1 MTR_8g467340 52.542 59 26 1 32 88 57 115 4.95e-15 73.2
MS.gene008887.t1 MTR_8g442330 76.316 38 9 0 48 85 14 51 5.19e-15 69.3
MS.gene008887.t1 MTR_6g012280 53.846 52 22 1 39 88 91 142 2.56e-14 70.9
MS.gene008887.t1 MTR_7g010300 51.852 54 24 1 37 88 86 139 4.80e-14 70.1
MS.gene008887.t1 MTR_6g012220 53.125 64 26 2 37 100 19 78 1.32e-13 64.3
MS.gene008887.t1 MTR_6g073013 41.538 65 37 1 39 102 19 83 8.59e-13 64.3
MS.gene008887.t1 MTR_7g070643 44.776 67 36 1 12 77 54 120 2.74e-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.gene008887.t1 AT4G24660 51.899 79 34 2 36 112 46 122 1.34e-23 94.4
MS.gene008887.t1 AT4G24660 51.899 79 34 2 36 112 46 122 1.43e-23 94.4
MS.gene008887.t1 AT1G75240 65.385 52 18 0 37 88 74 125 8.12e-21 88.6
MS.gene008887.t1 AT2G02540 58.491 53 22 0 37 89 85 137 2.00e-20 87.4
MS.gene008887.t1 AT2G02540 58.491 53 22 0 37 89 85 137 2.00e-20 87.4
MS.gene008887.t1 AT1G74660 64.151 53 19 0 37 89 37 89 5.32e-20 81.3
MS.gene008887.t1 AT1G74660 64.151 53 19 0 37 89 37 89 7.94e-20 81.3
MS.gene008887.t1 AT5G65410 66.038 53 18 0 36 88 72 124 1.43e-19 84.7
MS.gene008887.t1 AT1G14440 59.615 52 21 0 37 88 88 139 2.08e-19 84.7
MS.gene008887.t1 AT1G14440 59.615 52 21 0 37 88 88 139 2.08e-19 84.7
MS.gene008887.t1 AT3G50890 61.538 52 20 0 37 88 58 109 3.03e-19 83.2
MS.gene008887.t1 AT2G18350 58.491 53 22 0 36 88 79 131 2.93e-17 78.2
MS.gene008887.t1 AT3G28917 56.604 53 22 1 37 88 31 83 1.67e-16 72.4
MS.gene008887.t1 AT5G15210 48.611 72 28 3 22 88 40 107 9.33e-15 71.6
MS.gene008887.t1 AT1G18835 57.692 52 19 1 37 88 24 72 9.69e-15 67.4
MS.gene008887.t1 AT1G69600 31.507 146 79 4 11 152 3 131 2.19e-14 70.1
MS.gene008887.t1 AT3G28920 43.902 82 34 2 36 115 49 120 8.22e-14 69.3
MS.gene008887.t1 AT5G60480 49.180 61 23 2 32 87 30 87 5.65e-12 63.2
MS.gene008887.t1 AT5G39760 50.000 56 26 1 35 88 52 107 1.49e-11 62.8

Find 41 sgRNAs with CRISPR-Local

Find 61 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTCTGAAGCAAATAGTTTAC+AGG 0.318195 8.1:-35893021 MS.gene008887:CDS
CACAATCTAAGAAGAGATTC+AGG 0.367997 8.1:-35892609 MS.gene008887:CDS
GCTGGTATTGGTGGTGGTGG+TGG 0.379831 8.1:-35892646 MS.gene008887:CDS
TGAGAGCCTATCAATATTGC+TGG 0.395778 8.1:-35892664 MS.gene008887:CDS
CAAAGATAGAGGTGGAGAAT+TGG 0.404534 8.1:+35892743 None:intergenic
CCACCTCTATCTTTGTATGA+AGG 0.411052 8.1:-35892735 MS.gene008887:CDS
CCTATCAATATTGCTGGTAT+TGG 0.420072 8.1:-35892658 MS.gene008887:CDS
CTAAGAAGAGATTCAGGTCT+AGG 0.422419 8.1:-35892603 MS.gene008887:CDS
ATCAATATTGCTGGTATTGG+TGG 0.423701 8.1:-35892655 MS.gene008887:CDS
AAGAACCATGCTTCCAGCAT+TGG 0.428212 8.1:-35892978 MS.gene008887:CDS
CACCTCTATCTTTGTATGAA+GGG 0.435863 8.1:-35892734 MS.gene008887:CDS
CCAATACCAGCAATATTGAT+AGG 0.451941 8.1:+35892658 None:intergenic
ATTGGAGGTTATGCCGTTGA+TGG 0.455927 8.1:-35892960 MS.gene008887:CDS
CTTGGTGCTCCAGTCGTAGA+AGG 0.459839 8.1:+35892774 None:intergenic
ACTCATCACTTCGCTGACTT+TGG 0.460120 8.1:+35893094 None:intergenic
CATCACTTCGCTGACTTTGG+TGG 0.466785 8.1:+35893097 None:intergenic
CATGGAGCACTAAACGAGAT+AGG 0.482608 8.1:+35892816 None:intergenic
ACCTCTATCTTTGTATGAAG+GGG 0.485817 8.1:-35892733 MS.gene008887:CDS
GGAGAATTGGTTGTGCCCCT+TGG 0.489769 8.1:+35892756 None:intergenic
AACGGCATAACCTCCAATGC+TGG 0.490028 8.1:+35892965 None:intergenic
ATTGCTGGTATTGGTGGTGG+TGG 0.490450 8.1:-35892649 MS.gene008887:CDS
AGGTTGGAAGATTCCGAAAA+GGG 0.512733 8.1:-35892533 MS.gene008887:CDS
TAGAAGGAGTAACTGCTTGA+GGG 0.527054 8.1:+35892790 None:intergenic
AACCATGCTTCCAGCATTGG+AGG 0.529576 8.1:-35892975 MS.gene008887:CDS
GAGGTTGGAAGATTCCGAAA+AGG 0.538054 8.1:-35892534 MS.gene008887:CDS
AACCTCCAATGCTGGAAGCA+TGG 0.548110 8.1:+35892973 None:intergenic
TTCTACGACTGGAGCACCAA+GGG 0.559075 8.1:-35892772 MS.gene008887:CDS
AATATTGCTGGTATTGGTGG+TGG 0.560520 8.1:-35892652 MS.gene008887:CDS
GCAGTTACTCCTTCTACGAC+TGG 0.562065 8.1:-35892783 MS.gene008887:CDS
GTAGAAGGAGTAACTGCTTG+AGG 0.569241 8.1:+35892789 None:intergenic
AATGTACCTTCATCTCCAGC+AGG 0.574198 8.1:+35892921 None:intergenic
GTAACTGCTTGAGGGAGGCA+TGG 0.581241 8.1:+35892798 None:intergenic
CAACGACAGTTTCCTTCCTG+TGG 0.597037 8.1:+35892856 None:intergenic
CAGCAAAGAAAAGATGGTGA+TGG 0.612071 8.1:-35893120 None:intergenic
AAACTCACAACAACCATCAA+CGG 0.619715 8.1:+35892947 None:intergenic
AAGGGATGAGAATGTTGTCA+AGG 0.636812 8.1:-35892515 MS.gene008887:CDS
CTTCTACGACTGGAGCACCA+AGG 0.637408 8.1:-35892773 MS.gene008887:CDS
CCTTCATACAAAGATAGAGG+TGG 0.648904 8.1:+35892735 None:intergenic
CCTCTATCTTTGTATGAAGG+GGG 0.651375 8.1:-35892732 MS.gene008887:CDS
AAGGAGTAACTGCTTGAGGG+AGG 0.663240 8.1:+35892793 None:intergenic
TCTACGACTGGAGCACCAAG+GGG 0.703811 8.1:-35892771 MS.gene008887:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! ACATTAGAGTTTTTTAAATG+TGG - chr8.1:35892695-35892714 MS.gene008887:CDS 20.0%
!!! TAGTTTACAGGTAAATTTTA+AGG - chr8.1:35892589-35892608 MS.gene008887:CDS 20.0%
ATTGTCATAAAAACTTCCAC+AGG - chr8.1:35892726-35892745 MS.gene008887:CDS 30.0%
! AAAAGATGCTTGATTTTGCT+TGG - chr8.1:35893037-35893056 MS.gene008887:CDS 30.0%
! AAAGATGCTTGATTTTGCTT+GGG - chr8.1:35893038-35893057 MS.gene008887:CDS 30.0%
!! AAGGAGTTTTGTAATGAGAT+TGG - chr8.1:35893102-35893121 MS.gene008887:CDS 30.0%
!! AGGAGTTTTGTAATGAGATT+GGG - chr8.1:35893103-35893122 MS.gene008887:CDS 30.0%
!! TTCTGAAGCAAATAGTTTAC+AGG - chr8.1:35892577-35892596 MS.gene008887:CDS 30.0%
AAACTCACAACAACCATCAA+CGG + chr8.1:35892654-35892673 None:intergenic 35.0%
ACCTCTATCTTTGTATGAAG+GGG - chr8.1:35892865-35892884 MS.gene008887:CDS 35.0%
CACAATCTAAGAAGAGATTC+AGG - chr8.1:35892989-35893008 MS.gene008887:CDS 35.0%
CACCTCTATCTTTGTATGAA+GGG - chr8.1:35892864-35892883 MS.gene008887:CDS 35.0%
CCAATACCAGCAATATTGAT+AGG + chr8.1:35892943-35892962 None:intergenic 35.0%
CCTATCAATATTGCTGGTAT+TGG - chr8.1:35892940-35892959 MS.gene008887:CDS 35.0%
TCATAAAAACTTCCACAGGA+AGG - chr8.1:35892730-35892749 MS.gene008887:CDS 35.0%
! ACAACATTCTCATCCCTTTT+CGG + chr8.1:35893081-35893100 None:intergenic 35.0%
! ATCAATATTGCTGGTATTGG+TGG - chr8.1:35892943-35892962 MS.gene008887:CDS 35.0%
!! GGAGTTTTGTAATGAGATTG+GGG - chr8.1:35893104-35893123 MS.gene008887:CDS 35.0%
AAGGGATGAGAATGTTGTCA+AGG - chr8.1:35893083-35893102 MS.gene008887:CDS 40.0%
AGGTTGGAAGATTCCGAAAA+GGG - chr8.1:35893065-35893084 MS.gene008887:CDS 40.0%
CAAAGATAGAGGTGGAGAAT+TGG + chr8.1:35892858-35892877 None:intergenic 40.0%
CCACCTCTATCTTTGTATGA+AGG - chr8.1:35892863-35892882 MS.gene008887:CDS 40.0%
CCTCTATCTTTGTATGAAGG+GGG - chr8.1:35892866-35892885 MS.gene008887:CDS 40.0%
CCTTCATACAAAGATAGAGG+TGG + chr8.1:35892866-35892885 None:intergenic 40.0%
CTAAGAAGAGATTCAGGTCT+AGG - chr8.1:35892995-35893014 MS.gene008887:CDS 40.0%
TAGAAGGAGTAACTGCTTGA+GGG + chr8.1:35892811-35892830 None:intergenic 40.0%
TGAGAGCCTATCAATATTGC+TGG - chr8.1:35892934-35892953 MS.gene008887:CDS 40.0%
! ATGAAGGGGGCTATATTTTG+AGG - chr8.1:35892879-35892898 MS.gene008887:CDS 40.0%
! TGTTGTGAGTTTTTACCTGC+TGG - chr8.1:35892662-35892681 MS.gene008887:CDS 40.0%
! TTTTTACCTGCTGGAGATGA+AGG - chr8.1:35892671-35892690 MS.gene008887:CDS 40.0%
!! AATATTGCTGGTATTGGTGG+TGG - chr8.1:35892946-35892965 MS.gene008887:CDS 40.0%
!! TGAAGGGGGCTATATTTTGA+GGG - chr8.1:35892880-35892899 MS.gene008887:CDS 40.0%
AAGAACCATGCTTCCAGCAT+TGG - chr8.1:35892620-35892639 MS.gene008887:CDS 45.0%
AATGTACCTTCATCTCCAGC+AGG + chr8.1:35892680-35892699 None:intergenic 45.0%
ATTGGAGGTTATGCCGTTGA+TGG - chr8.1:35892638-35892657 MS.gene008887:CDS 45.0%
CCCCCTTCATACAAAGATAG+AGG + chr8.1:35892869-35892888 None:intergenic 45.0%
GAGGTTGGAAGATTCCGAAA+AGG - chr8.1:35893064-35893083 MS.gene008887:CDS 45.0%
GTAGAAGGAGTAACTGCTTG+AGG + chr8.1:35892812-35892831 None:intergenic 45.0%
! CATGGAGCACTAAACGAGAT+AGG + chr8.1:35892785-35892804 None:intergenic 45.0%
!! ACTCATCACTTCGCTGACTT+TGG + chr8.1:35892507-35892526 None:intergenic 45.0%
AACCTCCAATGCTGGAAGCA+TGG + chr8.1:35892628-35892647 None:intergenic 50.0%
AACGGCATAACCTCCAATGC+TGG + chr8.1:35892636-35892655 None:intergenic 50.0%
AAGGAGTAACTGCTTGAGGG+AGG + chr8.1:35892808-35892827 None:intergenic 50.0%
CAACGACAGTTTCCTTCCTG+TGG + chr8.1:35892745-35892764 None:intergenic 50.0%
GCAGTTACTCCTTCTACGAC+TGG - chr8.1:35892815-35892834 MS.gene008887:CDS 50.0%
! AACCATGCTTCCAGCATTGG+AGG - chr8.1:35892623-35892642 MS.gene008887:CDS 50.0%
! ATTTTGCTTGGGCACGAGGT+TGG - chr8.1:35893049-35893068 MS.gene008887:CDS 50.0%
! CTTGATTTTGCTTGGGCACG+AGG - chr8.1:35893045-35893064 MS.gene008887:CDS 50.0%
! TTCTACGACTGGAGCACCAA+GGG - chr8.1:35892826-35892845 MS.gene008887:CDS 50.0%
!! AGGGGGCTATATTTTGAGGG+AGG - chr8.1:35892883-35892902 MS.gene008887:CDS 50.0%
!! ATTGCTGGTATTGGTGGTGG+TGG - chr8.1:35892949-35892968 MS.gene008887:CDS 50.0%
!! CATCACTTCGCTGACTTTGG+TGG + chr8.1:35892504-35892523 None:intergenic 50.0%
GGAGAATTGGTTGTGCCCCT+TGG + chr8.1:35892845-35892864 None:intergenic 55.0%
GTAACTGCTTGAGGGAGGCA+TGG + chr8.1:35892803-35892822 None:intergenic 55.0%
! CTTCTACGACTGGAGCACCA+AGG - chr8.1:35892825-35892844 MS.gene008887:CDS 55.0%
! TCTACGACTGGAGCACCAAG+GGG - chr8.1:35892827-35892846 MS.gene008887:CDS 55.0%
!! CTTGGTGCTCCAGTCGTAGA+AGG + chr8.1:35892827-35892846 None:intergenic 55.0%
!! GCTGGTATTGGTGGTGGTGG+TGG - chr8.1:35892952-35892971 MS.gene008887:CDS 60.0%
!! GGTATTGGTGGTGGTGGTGG+TGG - chr8.1:35892955-35892974 MS.gene008887:CDS 60.0%
!! GTGGTGGTGGTGGTGGAGAA+GGG - chr8.1:35892962-35892981 MS.gene008887:CDS 60.0%
!! GGTGGTGGTGGTGGTGGAGA+AGG - chr8.1:35892961-35892980 MS.gene008887:CDS 65.0%


Chromosome Type Strat End Strand Name
chr8.1 gene 35892491 35893129 35892491 ID=MS.gene008887
chr8.1 mRNA 35892491 35893129 35892491 ID=MS.gene008887.t1;Parent=MS.gene008887
chr8.1 exon 35892491 35893129 35892491 ID=MS.gene008887.t1.exon1;Parent=MS.gene008887.t1
chr8.1 CDS 35892491 35893129 35892491 ID=cds.MS.gene008887.t1;Parent=MS.gene008887.t1
Gene Sequence

>MS.gene008887

ATGGTGATGGCCACCAAAGTCAGCGAAGTGATGAGTAGCACATCACAAGAGAAAATATCAACTCGAGTAGAAGAATCTCATATGAATTCTGAAGCAAATAGTTTACAGGTAAATTTTAAGGAATGTTTGAAGAACCATGCTTCCAGCATTGGAGGTTATGCCGTTGATGGTTGTTGTGAGTTTTTACCTGCTGGAGATGAAGGTACATTAGAGTTTTTTAAATGTGGTGCTTGTGATTGTCATAAAAACTTCCACAGGAAGGAAACTGTCGTTGTTTCTAGAGATATGACTCCTATCTCGTTTAGTGCTCCATGCCTCCCTCAAGCAGTTACTCCTTCTACGACTGGAGCACCAAGGGGCACAACCAATTCTCCACCTCTATCTTTGTATGAAGGGGGCTATATTTTGAGGGAGGATCTTGAACAAAATGTTCATCATGTTGTTGAGAGCCTATCAATATTGCTGGTATTGGTGGTGGTGGTGGTGGAGAAGGGTCATCACAATCTAAGAAGAGATTCAGGTCTAGGTTCACACATGAACAAAGAGAAAAGATGCTTGATTTTGCTTGGGCACGAGGTTGGAAGATTCCGAAAAGGGATGAGAATGTTGTCAAGGAGTTTTGTAATGAGATTGGGGTGA
Protein sequence

>MS.gene008887.t1

MVMATKVSEVMSSTSQEKISTRVEESHMNSEANSLQVNFKECLKNHASSIGGYAVDGCCEFLPAGDEGTLEFFKCGACDCHKNFHRKETVVVSRDMTPISFSAPCLPQAVTPSTTGAPRGTTNSPPLSLYEGGYILREDLEQNVHHVVESLSILLVLVVVVVEKGHHNLRRDSGLGSHMNKEKRCLILLGHEVGRFRKGMRMLSRSFVMRLG