AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene21026

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene21026.t1 MTR_1g084060 96.063 127 4 1 1 126 1 127 4.17e-86 252
MS.gene21026.t1 MTR_1g084060 96.063 127 4 1 1 126 1 127 2.67e-85 251
MS.gene21026.t1 MTR_5g033720 52.101 119 49 2 9 121 63 179 2.13e-36 126
MS.gene21026.t1 MTR_5g085860 44.828 116 56 1 19 126 47 162 9.41e-26 98.6
MS.gene21026.t1 MTR_1g017080 46.602 103 49 2 18 115 119 220 1.14e-23 94.0
MS.gene21026.t1 MTR_2g024390 46.789 109 51 2 18 122 117 222 8.17e-23 91.7
MS.gene21026.t1 MTR_6g071190 34.906 106 67 1 15 120 39 142 6.65e-14 64.7
MS.gene21026.t1 MTR_1g032750 29.167 120 67 2 6 115 10 121 1.67e-11 57.8
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene21026.t1 AT1G70510 50.450 111 47 2 17 121 68 176 8.51e-35 122
MS.gene21026.t1 AT1G23380 50.459 109 44 2 17 118 84 189 1.05e-32 117
MS.gene21026.t1 AT1G70510 48.696 115 47 3 17 121 68 180 1.57e-32 116
MS.gene21026.t1 AT1G23380 49.550 111 44 3 17 118 84 191 9.31e-31 112
MS.gene21026.t1 AT1G62360 46.875 96 47 1 18 109 121 216 4.00e-22 90.1
MS.gene21026.t1 AT4G08150 39.806 103 57 1 18 115 134 236 3.14e-21 87.8

Find 28 sgRNAs with CRISPR-Local

Find 40 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GCTTCTCTTCTTGAAGAAAT+AGG 0.173162 1.4:+68960591 MS.gene21026:CDS
TCTCACGGAAAGCATTATTT+TGG 0.227729 1.4:-68960626 None:intergenic
CTTCTCTTCTTGAAGAAATA+GGG 0.308161 1.4:+68960592 MS.gene21026:CDS
ACAACCAATCGGATCTAATA+AGG 0.325364 1.4:+68960240 MS.gene21026:CDS
TTTACCTGAACGGTTGTAAT+CGG 0.376328 1.4:-68960974 None:intergenic
TGTTGCTTCATTGAAGGGCT+TGG 0.378477 1.4:-68960887 None:intergenic
AATAATGCTTTCCGTGAGAT+AGG 0.392343 1.4:+68960630 MS.gene21026:CDS
GATAGTAGATTTGGATAAAG+AGG 0.394577 1.4:-68960308 None:intergenic
TCCTGACCTTGACCACTTCA+TGG 0.397547 1.4:+68960659 MS.gene21026:CDS
AAATAATGTTGCTTCATTGA+AGG 0.405931 1.4:-68960893 None:intergenic
AATAATGTTGCTTCATTGAA+GGG 0.423656 1.4:-68960892 None:intergenic
TCATCCGATTACAACCGTTC+AGG 0.455239 1.4:+68960970 MS.gene21026:CDS
ACCATGAAGTGGTCAAGGTC+AGG 0.484448 1.4:-68960660 None:intergenic
AAAGAGGGTGAGTTGCGATC+TGG 0.510035 1.4:-68960292 None:intergenic
TCTAATAAGGTTGGATATGA+CGG 0.529171 1.4:+68960253 MS.gene21026:CDS
AGAAGAGAAGCAAGTTCTGT+TGG 0.544757 1.4:-68960579 None:intergenic
ATAGTAGATTTGGATAAAGA+GGG 0.546531 1.4:-68960307 None:intergenic
CCAATCGGATCTAATAAGGT+TGG 0.547810 1.4:+68960244 MS.gene21026:CDS
CCAACCTTATTAGATCCGAT+TGG 0.554336 1.4:-68960244 None:intergenic
ACAACTAAACGAACTTTGCA+AGG 0.560050 1.4:+68960933 MS.gene21026:CDS
TCACATGGAACACAACCAAT+CGG 0.562048 1.4:+68960229 None:intergenic
TTAAGTTCTCTTTACCTGAA+CGG 0.565840 1.4:-68960984 None:intergenic
AATATACCATGAAGTGGTCA+AGG 0.574865 1.4:-68960665 None:intergenic
TAAAAGAATATACCATGAAG+TGG 0.580028 1.4:-68960671 None:intergenic
CAGGATCATCTCCTATCTCA+CGG 0.597806 1.4:-68960641 None:intergenic
CAACTAAACGAACTTTGCAA+GGG 0.626350 1.4:+68960934 MS.gene21026:CDS
AACTAAACGAACTTTGCAAG+GGG 0.629556 1.4:+68960935 MS.gene21026:CDS
AGTTCTTCATAGATACAAAG+AGG 0.649236 1.4:+68960858 MS.gene21026:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAAAAAATATAGTAGAAAAT+TGG - chr1.4:68960718-68960737 None:intergenic 10.0%
!! AAATATATATGATGAATTAA+AGG - chr1.4:68960376-68960395 None:intergenic 10.0%
!! ATTACATTAATTAAATCAGA+TGG + chr1.4:68960738-68960757 MS.gene21026:intron 15.0%
!!! ATATAGAATAAAAAACCTTT+TGG - chr1.4:68960349-68960368 None:intergenic 15.0%
!! ATTAATTAAATCAGATGGAA+TGG + chr1.4:68960743-68960762 MS.gene21026:intron 20.0%
!! ATTTATTACACTTTGTGATT+AGG + chr1.4:68960822-68960841 MS.gene21026:intron 20.0%
!! TATATATGATGAATTAAAGG+AGG - chr1.4:68960373-68960392 None:intergenic 20.0%
!!! ATATTTTTCACTCAATCATA+TGG + chr1.4:68960390-68960409 MS.gene21026:intron 20.0%
! AAAAAAGCAGATAGTAGATT+TGG - chr1.4:68960320-68960339 None:intergenic 25.0%
! ATACTATATATTGTGCATGA+AGG + chr1.4:68960548-68960567 MS.gene21026:intron 25.0%
! ATAGTAGATTTGGATAAAGA+GGG - chr1.4:68960310-68960329 None:intergenic 25.0%
! ATATAGTAGAAAATTGGACT+TGG - chr1.4:68960712-68960731 None:intergenic 25.0%
! TAAAAGAATATACCATGAAG+TGG - chr1.4:68960674-68960693 None:intergenic 25.0%
!! AAATAATGTTGCTTCATTGA+AGG - chr1.4:68960896-68960915 None:intergenic 25.0%
!! AATAATGTTGCTTCATTGAA+GGG - chr1.4:68960895-68960914 None:intergenic 25.0%
AGTTCTTCATAGATACAAAG+AGG + chr1.4:68960858-68960877 MS.gene21026:CDS 30.0%
ATATATTGTGCATGAAGGTT+GGG + chr1.4:68960553-68960572 MS.gene21026:intron 30.0%
CTTCTCTTCTTGAAGAAATA+GGG + chr1.4:68960592-68960611 MS.gene21026:CDS 30.0%
GATAGTAGATTTGGATAAAG+AGG - chr1.4:68960311-68960330 None:intergenic 30.0%
TATATATTGTGCATGAAGGT+TGG + chr1.4:68960552-68960571 MS.gene21026:intron 30.0%
TCTAATAAGGTTGGATATGA+CGG + chr1.4:68960253-68960272 MS.gene21026:CDS 30.0%
!!! TGCTTTTTTAGAATGCCAAA+AGG + chr1.4:68960331-68960350 MS.gene21026:CDS 30.0%
AACTAAACGAACTTTGCAAG+GGG + chr1.4:68960935-68960954 MS.gene21026:CDS 35.0%
AATAATGCTTTCCGTGAGAT+AGG + chr1.4:68960630-68960649 MS.gene21026:CDS 35.0%
AATATACCATGAAGTGGTCA+AGG - chr1.4:68960668-68960687 None:intergenic 35.0%
ACAACCAATCGGATCTAATA+AGG + chr1.4:68960240-68960259 MS.gene21026:CDS 35.0%
ACAACTAAACGAACTTTGCA+AGG + chr1.4:68960933-68960952 MS.gene21026:CDS 35.0%
CAACTAAACGAACTTTGCAA+GGG + chr1.4:68960934-68960953 MS.gene21026:CDS 35.0%
GCTTCTCTTCTTGAAGAAAT+AGG + chr1.4:68960591-68960610 MS.gene21026:CDS 35.0%
TATATTGTGCATGAAGGTTG+GGG + chr1.4:68960554-68960573 MS.gene21026:intron 35.0%
!!! TCTCACGGAAAGCATTATTT+TGG - chr1.4:68960629-68960648 None:intergenic 35.0%
AGAAGAGAAGCAAGTTCTGT+TGG - chr1.4:68960582-68960601 None:intergenic 40.0%
CCAACCTTATTAGATCCGAT+TGG - chr1.4:68960247-68960266 None:intergenic 40.0%
CCAATCGGATCTAATAAGGT+TGG + chr1.4:68960244-68960263 MS.gene21026:CDS 40.0%
!!! CACGGAAAGCATTATTTTGG+TGG - chr1.4:68960626-68960645 None:intergenic 40.0%
CAGGATCATCTCCTATCTCA+CGG - chr1.4:68960644-68960663 None:intergenic 45.0%
! TGTTGCTTCATTGAAGGGCT+TGG - chr1.4:68960890-68960909 None:intergenic 45.0%
AAAGAGGGTGAGTTGCGATC+TGG - chr1.4:68960295-68960314 None:intergenic 50.0%
ACCATGAAGTGGTCAAGGTC+AGG - chr1.4:68960663-68960682 None:intergenic 50.0%
TCCTGACCTTGACCACTTCA+TGG + chr1.4:68960659-68960678 MS.gene21026:CDS 50.0%


Chromosome Type Strat End Strand Name
chr1.4 gene 68960233 68960991 68960233 ID=MS.gene21026
chr1.4 mRNA 68960233 68960991 68960233 ID=MS.gene21026.t1;Parent=MS.gene21026
chr1.4 exon 68960233 68960352 68960233 ID=MS.gene21026.t1.exon1;Parent=MS.gene21026.t1
chr1.4 CDS 68960233 68960352 68960233 ID=cds.MS.gene21026.t1;Parent=MS.gene21026.t1
chr1.4 exon 68960570 68960680 68960570 ID=MS.gene21026.t1.exon2;Parent=MS.gene21026.t1
chr1.4 CDS 68960570 68960680 68960570 ID=cds.MS.gene21026.t1;Parent=MS.gene21026.t1
chr1.4 exon 68960844 68960991 68960844 ID=MS.gene21026.t1.exon3;Parent=MS.gene21026.t1
chr1.4 CDS 68960844 68960991 68960844 ID=cds.MS.gene21026.t1;Parent=MS.gene21026.t1
Gene Sequence

>MS.gene21026

ATGGAACACAACCAATCGGATCTAATAAGGTTGGATATGACGGATCGAATTATCAAGAACCAGATCGCAACTCACCCTCTTTATCCAAATCTACTATCTGCTTTTTTAGAATGCCAAAAGGTTTTTTATTCTATATACCTCCTTTAATTCATCATATATATTTTTCACTCAATCATATGGTTAGTATTATTGTTGTTACTATTATTATAAATATTAATTAATTCTTAGCTAACATGCTTTATATTTTATTCTTTTATAGTATGATTAGTTTATTTATATATTAAAATTAAATAATCTAATTTTGTATTCATATGAATACTATATATTGTGCATGAAGGTTGGGGCACCAACAGAACTTGCTTCTCTTCTTGAAGAAATAGGGCGTGAAAACCACCAAAATAATGCTTTCCGTGAGATAGGAGATGATCCTGACCTTGACCACTTCATGGTATATTCTTTTAAGTAATTTATTTTTTCCAAGTCCAATTTTCTACTATATTTTTTTATTACATTAATTAAATCAGATGGAATGGATAGACTTAAGAAATGCATATGTTATATTTAATGTTGTTACTGTTGCTAACATTTAATTTATTACACTTTGTGATTAGGAATCATACTGTGAAGTTCTTCATAGATACAAAGAGGAGTTATCCAAGCCCTTCAATGAAGCAACATTATTTTTGTGCAATATTGAATCACAACTAAACGAACTTTGCAAGGGGACACAAACAATGTCATCCGATTACAACCGTTCAG
Protein sequence

>MS.gene21026.t1

MEHNQSDLIRLDMTDRIIKNQIATHPLYPNLLSAFLECQKVGAPTELASLLEEIGRENHQNNAFREIGDDPDLDHFMESYCEVLHRYKEELSKPFNEATLFLCNIESQLNELCKGTQTMSSDYNRS