AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene065613

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene065613.t1 MTR_6g059530 86.207 203 26 1 1 201 1 203 2.46e-115 327
MS.gene065613.t1 MTR_6g059410 85.222 203 27 2 1 201 1 202 6.64e-112 318
MS.gene065613.t1 MTR_6g059650 57.216 194 73 5 17 201 19 211 2.56e-66 202
MS.gene065613.t1 MTR_6g065460 53.659 205 82 6 1 193 1 204 2.92e-55 174
MS.gene065613.t1 MTR_6g059760 48.113 212 87 12 1 196 1 205 7.21e-47 153
MS.gene065613.t1 MTR_6g065460 49.000 200 75 6 1 193 1 180 1.30e-45 149
MS.gene065613.t1 MTR_6g044780 43.662 213 105 9 1 199 1 212 2.19e-41 140
MS.gene065613.t1 MTR_6g044810 41.784 213 109 8 1 199 1 212 1.18e-39 135
MS.gene065613.t1 MTR_3g463590 43.750 192 95 7 20 201 23 211 4.94e-39 133
MS.gene065613.t1 MTR_6g059680 46.500 200 88 8 18 201 20 216 8.86e-39 133
MS.gene065613.t1 MTR_6g045097 42.254 213 108 9 1 199 1 212 1.28e-38 132
MS.gene065613.t1 MTR_6g045403 41.038 212 110 8 1 199 1 210 1.50e-36 127
MS.gene065613.t1 MTR_6g059730 45.581 215 100 10 1 201 1 212 5.76e-36 125
MS.gene065613.t1 MTR_6g009650 41.827 208 102 9 1 194 1 203 9.18e-35 122
MS.gene065613.t1 MTR_6g017225 40.359 223 104 13 1 201 1 216 1.07e-33 123
MS.gene065613.t1 MTR_6g045433 36.681 229 107 10 1 201 1 219 1.66e-32 117
MS.gene065613.t1 MTR_6g066190 39.614 207 106 9 1 193 1 202 2.39e-32 116
MS.gene065613.t1 MTR_6g009563 39.524 210 105 9 1 194 1 204 2.79e-31 113
MS.gene065613.t1 MTR_6g066210 39.070 215 110 10 1 199 1 210 3.00e-29 108
MS.gene065613.t1 MTR_6g059810 37.681 207 103 9 4 190 8 208 2.99e-28 105
MS.gene065613.t1 MTR_1g035770 37.073 205 109 8 6 192 7 209 5.62e-28 105
MS.gene065613.t1 MTR_6g059755 49.074 108 49 4 98 199 18 125 7.04e-25 94.7
MS.gene065613.t1 MTR_6g078070 31.731 208 122 8 1 193 1 203 1.06e-19 83.2
MS.gene065613.t1 MTR_6g078100 32.850 207 123 8 1 193 1 205 3.45e-18 79.3
MS.gene065613.t1 MTR_6g065570 55.932 59 23 1 17 72 15 73 4.15e-17 73.6
MS.gene065613.t1 MTR_0302s0030 29.187 209 115 7 5 190 1 199 2.52e-13 66.2
MS.gene065613.t1 MTR_3g106585 31.313 198 123 9 5 194 6 198 9.13e-13 64.7
MS.gene065613.t1 MTR_0100s0150 28.846 208 116 8 5 190 1 198 1.56e-12 63.9
MS.gene065613.t1 MTR_2g073010 30.151 199 127 7 1 193 6 198 1.76e-11 60.8
MS.gene065613.t1 MTR_6g078290 29.756 205 114 9 11 190 10 209 2.43e-11 60.8
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene065613.t1 AT1G73260 33.981 206 112 9 5 197 15 209 4.75e-21 87.0
MS.gene065613.t1 AT1G17860 32.044 181 106 8 21 193 24 195 2.61e-15 71.2

Find 48 sgRNAs with CRISPR-Local

Find 59 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ACTATATTGCACCACTTATC+TGG 0.191488 6.3:+63688811 MS.gene065613:CDS
CAACTGAAAATGATCCCTTT+AGG 0.293355 6.3:+63689231 MS.gene065613:CDS
AACTGAAAATGATCCCTTTA+GGG 0.300397 6.3:+63689232 MS.gene065613:CDS
CCTACACCTTGGGTTGGTAT+TGG 0.305524 6.3:+63689056 MS.gene065613:CDS
GGTAAGTAATGTTGGCTTCA+TGG 0.309270 6.3:-63688691 None:intergenic
GAAACAGTTGAAGACATAAA+TGG 0.316517 6.3:+63688762 MS.gene065613:CDS
AAATCTTGAAGAACAGTAAC+TGG 0.358169 6.3:-63688885 None:intergenic
AATGGAAACCCCGTATTTCC+TGG 0.358580 6.3:+63688780 MS.gene065613:CDS
ACTCGTATGTTAAATCTAAC+TGG 0.363967 6.3:-63688930 None:intergenic
ACTGTTTCAGTAAAAGCTAA+TGG 0.364363 6.3:-63688747 None:intergenic
AAAATTAAGACAATTGGTTC+AGG 0.369696 6.3:+63689110 MS.gene065613:CDS
CCTGGTGGTTGTAGTGATAT+TGG 0.387244 6.3:+63689173 MS.gene065613:CDS
TGATGATTTCCCTACACCTT+GGG 0.392597 6.3:+63689046 MS.gene065613:CDS
TCATTTAAAATTAAGACAAT+TGG 0.397855 6.3:+63689104 MS.gene065613:CDS
TTGGCAGATTCAGCACAGTT+TGG 0.422008 6.3:-63689008 None:intergenic
ATCTGGGGAGCAGGAGGTGG+TGG 0.433696 6.3:+63688828 MS.gene065613:CDS
AGAGAAAAGGTAAGTAATGT+TGG 0.440708 6.3:-63688699 None:intergenic
CTATATTGCACCACTTATCT+GGG 0.458103 6.3:+63688812 MS.gene065613:CDS
GATAATATTGACGCAATTGA+AGG 0.458780 6.3:+63689080 MS.gene065613:CDS
CTGTGCTGAATCTGCCAAAT+GGG 0.460200 6.3:+63689013 MS.gene065613:CDS
ATCATGAGCTAGAACCCATT+TGG 0.471454 6.3:-63689027 None:intergenic
AGATGAGAATGGATGGCGTT+TGG 0.471954 6.3:+63689205 MS.gene065613:CDS
CTGGTGGTTGTAGTGATATT+GGG 0.472823 6.3:+63689174 MS.gene065613:CDS
ACTGTGCTGAATCTGCCAAA+TGG 0.476531 6.3:+63689012 MS.gene065613:CDS
AGTAAAAGCTAATGGAAAGT+AGG 0.481391 6.3:-63688739 None:intergenic
TGGAGATTTGATTCAGACTA+CGG 0.487047 6.3:-63689288 None:intergenic
GGAAAAGAGGAGGAGAGAAA+AGG 0.488375 6.3:-63688712 None:intergenic
GAAAGTAGGCAAAGGAAAAG+AGG 0.491486 6.3:-63688725 None:intergenic
CTTATCTGGGGAGCAGGAGG+TGG 0.493336 6.3:+63688825 MS.gene065613:CDS
GCACCACTTATCTGGGGAGC+AGG 0.501214 6.3:+63688819 MS.gene065613:CDS
ATGATGATTTCCCTACACCT+TGG 0.506844 6.3:+63689045 MS.gene065613:CDS
GATTTCCCTACACCTTGGGT+TGG 0.516772 6.3:+63689050 MS.gene065613:CDS
CCAATACCAACCCAAGGTGT+AGG 0.518662 6.3:-63689056 None:intergenic
GGGAGGTATAGAGATGAGAA+TGG 0.518670 6.3:+63689194 MS.gene065613:CDS
TTTAACATACGAGTATTTCG+TGG 0.521492 6.3:+63688939 MS.gene065613:CDS
CCTCCTGCTCCCCAGATAAG+TGG 0.524330 6.3:-63688822 None:intergenic
GGATTGAAACTTGGTAGGAC+AGG 0.528578 6.3:+63688849 MS.gene065613:CDS
CAATACCAACCCAAGGTGTA+GGG 0.543524 6.3:-63689055 None:intergenic
AGTAGGCAAAGGAAAAGAGG+AGG 0.560366 6.3:-63688722 None:intergenic
GGAGGTGGTGGATTGAAACT+TGG 0.575753 6.3:+63688840 MS.gene065613:CDS
GGTATAGAGATGAGAATGGA+TGG 0.592483 6.3:+63689198 MS.gene065613:CDS
AGCTAATGGAAAGTAGGCAA+AGG 0.597478 6.3:-63688733 None:intergenic
CCACTTATCTGGGGAGCAGG+AGG 0.601917 6.3:+63688822 MS.gene065613:CDS
GTGGTGGATTGAAACTTGGT+AGG 0.627699 6.3:+63688844 MS.gene065613:CDS
CCAATATCACTACAACCACC+AGG 0.635878 6.3:-63689173 None:intergenic
TTATCACCAATACCAACCCA+AGG 0.671863 6.3:-63689062 None:intergenic
TATATTGCACCACTTATCTG+GGG 0.693225 6.3:+63688813 MS.gene065613:CDS
GTGGTTGTAGTGATATTGGG+AGG 0.715809 6.3:+63689177 MS.gene065613:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TCATTTAAAATTAAGACAAT+TGG + chr6.3:63689104-63689123 MS.gene065613:CDS 15.0%
!! AAAATTAAGACAATTGGTTC+AGG + chr6.3:63689110-63689129 MS.gene065613:CDS 25.0%
AAATCTTGAAGAACAGTAAC+TGG - chr6.3:63688888-63688907 None:intergenic 30.0%
AACTGAAAATGATCCCTTTA+GGG + chr6.3:63689232-63689251 MS.gene065613:CDS 30.0%
ACTCGTATGTTAAATCTAAC+TGG - chr6.3:63688933-63688952 None:intergenic 30.0%
ACTGTTTCAGTAAAAGCTAA+TGG - chr6.3:63688750-63688769 None:intergenic 30.0%
AGAGAAAAGGTAAGTAATGT+TGG - chr6.3:63688702-63688721 None:intergenic 30.0%
AGTAAAAGCTAATGGAAAGT+AGG - chr6.3:63688742-63688761 None:intergenic 30.0%
ATCAACAAAAACAACCCTAA+AGG - chr6.3:63689249-63689268 None:intergenic 30.0%
GAAACAGTTGAAGACATAAA+TGG + chr6.3:63688762-63688781 MS.gene065613:CDS 30.0%
GATAATATTGACGCAATTGA+AGG + chr6.3:63689080-63689099 MS.gene065613:CDS 30.0%
TCAACAAAAACAACCCTAAA+GGG - chr6.3:63689248-63689267 None:intergenic 30.0%
TTTAACATACGAGTATTTCG+TGG + chr6.3:63688939-63688958 MS.gene065613:CDS 30.0%
! TAAAGGGATCATTTTCAGTT+GGG - chr6.3:63689232-63689251 None:intergenic 30.0%
ACTATATTGCACCACTTATC+TGG + chr6.3:63688811-63688830 MS.gene065613:CDS 35.0%
CAACTGAAAATGATCCCTTT+AGG + chr6.3:63689231-63689250 MS.gene065613:CDS 35.0%
CTATATTGCACCACTTATCT+GGG + chr6.3:63688812-63688831 MS.gene065613:CDS 35.0%
TATATTGCACCACTTATCTG+GGG + chr6.3:63688813-63688832 MS.gene065613:CDS 35.0%
! CTAAAGGGATCATTTTCAGT+TGG - chr6.3:63689233-63689252 None:intergenic 35.0%
! GCAATATAGTATTTTCTGCC+AGG - chr6.3:63688801-63688820 None:intergenic 35.0%
! GTATTTTCTGCCAGGAAATA+CGG - chr6.3:63688793-63688812 None:intergenic 35.0%
! TATTTTCTGCCAGGAAATAC+GGG - chr6.3:63688792-63688811 None:intergenic 35.0%
! TGTTCTTCAAGATTTTCGTG+AGG + chr6.3:63688893-63688912 MS.gene065613:CDS 35.0%
AGCTAATGGAAAGTAGGCAA+AGG - chr6.3:63688736-63688755 None:intergenic 40.0%
ATCATGAGCTAGAACCCATT+TGG - chr6.3:63689030-63689049 None:intergenic 40.0%
ATGATGATTTCCCTACACCT+TGG + chr6.3:63689045-63689064 MS.gene065613:CDS 40.0%
CCAGGTCGATTACTGAAAAA+TGG - chr6.3:63689158-63689177 None:intergenic 40.0%
CTGGTGGTTGTAGTGATATT+GGG + chr6.3:63689174-63689193 MS.gene065613:CDS 40.0%
GAAAGTAGGCAAAGGAAAAG+AGG - chr6.3:63688728-63688747 None:intergenic 40.0%
GGTATAGAGATGAGAATGGA+TGG + chr6.3:63689198-63689217 MS.gene065613:CDS 40.0%
TGATGATTTCCCTACACCTT+GGG + chr6.3:63689046-63689065 MS.gene065613:CDS 40.0%
TTATCACCAATACCAACCCA+AGG - chr6.3:63689065-63689084 None:intergenic 40.0%
! ATTTTCTGCCAGGAAATACG+GGG - chr6.3:63688791-63688810 None:intergenic 40.0%
! GATTTTCGTGAGGTTGTTAG+AGG + chr6.3:63688903-63688922 MS.gene065613:CDS 40.0%
!! CCATTTTTCAGTAATCGACC+TGG + chr6.3:63689155-63689174 MS.gene065613:CDS 40.0%
!! TTTTTCAGTAATCGACCTGG+TGG + chr6.3:63689158-63689177 MS.gene065613:CDS 40.0%
AATGGAAACCCCGTATTTCC+TGG + chr6.3:63688780-63688799 MS.gene065613:CDS 45.0%
ACTGTGCTGAATCTGCCAAA+TGG + chr6.3:63689012-63689031 MS.gene065613:CDS 45.0%
AGATGAGAATGGATGGCGTT+TGG + chr6.3:63689205-63689224 MS.gene065613:CDS 45.0%
AGTAGGCAAAGGAAAAGAGG+AGG - chr6.3:63688725-63688744 None:intergenic 45.0%
CAATACCAACCCAAGGTGTA+GGG - chr6.3:63689058-63689077 None:intergenic 45.0%
CCAATATCACTACAACCACC+AGG - chr6.3:63689176-63689195 None:intergenic 45.0%
CCTGGTGGTTGTAGTGATAT+TGG + chr6.3:63689173-63689192 MS.gene065613:CDS 45.0%
CTGTGCTGAATCTGCCAAAT+GGG + chr6.3:63689013-63689032 MS.gene065613:CDS 45.0%
GGAAAAGAGGAGGAGAGAAA+AGG - chr6.3:63688715-63688734 None:intergenic 45.0%
GGATTGAAACTTGGTAGGAC+AGG + chr6.3:63688849-63688868 MS.gene065613:CDS 45.0%
GTGGTTGTAGTGATATTGGG+AGG + chr6.3:63689177-63689196 MS.gene065613:CDS 45.0%
TTGGCAGATTCAGCACAGTT+TGG - chr6.3:63689011-63689030 None:intergenic 45.0%
! GGGAGGTATAGAGATGAGAA+TGG + chr6.3:63689194-63689213 MS.gene065613:CDS 45.0%
!! GTGGTGGATTGAAACTTGGT+AGG + chr6.3:63688844-63688863 MS.gene065613:CDS 45.0%
CCAATACCAACCCAAGGTGT+AGG - chr6.3:63689059-63689078 None:intergenic 50.0%
GATTTCCCTACACCTTGGGT+TGG + chr6.3:63689050-63689069 MS.gene065613:CDS 50.0%
!! CCTACACCTTGGGTTGGTAT+TGG + chr6.3:63689056-63689075 MS.gene065613:CDS 50.0%
!! GGAGGTGGTGGATTGAAACT+TGG + chr6.3:63688840-63688859 MS.gene065613:CDS 50.0%
CCACTTATCTGGGGAGCAGG+AGG + chr6.3:63688822-63688841 MS.gene065613:CDS 60.0%
CCTCCTGCTCCCCAGATAAG+TGG - chr6.3:63688825-63688844 None:intergenic 60.0%
CTTATCTGGGGAGCAGGAGG+TGG + chr6.3:63688825-63688844 MS.gene065613:CDS 60.0%
GCACCACTTATCTGGGGAGC+AGG + chr6.3:63688819-63688838 MS.gene065613:CDS 60.0%
ATCTGGGGAGCAGGAGGTGG+TGG + chr6.3:63688828-63688847 MS.gene065613:CDS 65.0%


Chromosome Type Strat End Strand Name
chr6.3 gene 63688693 63689298 63688693 ID=MS.gene065613
chr6.3 mRNA 63688693 63689298 63688693 ID=MS.gene065613.t1;Parent=MS.gene065613
chr6.3 exon 63688693 63689298 63688693 ID=MS.gene065613.t1.exon1;Parent=MS.gene065613.t1
chr6.3 CDS 63688693 63689298 63688693 ID=cds.MS.gene065613.t1;Parent=MS.gene065613.t1
Gene Sequence

>MS.gene065613

ATGAAGCCAACATTACTTACCTTTTCTCTCCTCCTCTTTTCCTTTGCCTACTTTCCATTAGCTTTTACTGAAACAGTTGAAGACATAAATGGAAACCCCGTATTTCCTGGCAGAAAATACTATATTGCACCACTTATCTGGGGAGCAGGAGGTGGTGGATTGAAACTTGGTAGGACAGGAAACTCAGAATGTCCAGTTACTGTTCTTCAAGATTTTCGTGAGGTTGTTAGAGGCTTGCCAGTTAGATTTAACATACGAGTATTTCGTGGTGTTATCTTTACAACTGACGAAGTAGATATTGAGTTTGTTAAGAAACCAAACTGTGCTGAATCTGCCAAATGGGTTCTAGCTCATGATGATTTCCCTACACCTTGGGTTGGTATTGGTGATAATATTGACGCAATTGAAGGTTCATTTAAAATTAAGACAATTGGTTCAGGAGCATACAAGCTTGTGTATTGTCCATTTTTCAGTAATCGACCTGGTGGTTGTAGTGATATTGGGAGGTATAGAGATGAGAATGGATGGCGTTTGGTCCCAACTGAAAATGATCCCTTTAGGGTTGTTTTTGTTGATGCTAATGAATCTGAAAAAGCCGTAGTCTGA
Protein sequence

>MS.gene065613.t1

MKPTLLTFSLLLFSFAYFPLAFTETVEDINGNPVFPGRKYYIAPLIWGAGGGGLKLGRTGNSECPVTVLQDFREVVRGLPVRFNIRVFRGVIFTTDEVDIEFVKKPNCAESAKWVLAHDDFPTPWVGIGDNIDAIEGSFKIKTIGSGAYKLVYCPFFSNRPGGCSDIGRYRDENGWRLVPTENDPFRVVFVDANESEKAVV