AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene64862

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene64862.t1 MTR_5g023880 57.692 182 36 4 1 156 1 167 1.89e-59 183
MS.gene64862.t1 MTR_5g023900 54.286 175 60 2 1 155 1 175 1.08e-57 179
MS.gene64862.t1 MTR_5g023870 68.182 132 25 3 1 128 1 119 3.17e-55 170
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 66 sgRNAs with CRISPR-Local

Find 84 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GTTGAATTCTCGGAAGGGTT+AGG 0.289300 5.3:-13749863 None:intergenic
ATGAGGGGACTTGTTGTTGG+TGG 0.313710 5.3:-13749888 None:intergenic
GGGCTTCTTGATCGTCCTCT+TGG 0.324765 5.3:-13750795 None:intergenic
TGCTTATCAGTTGTATCGGC+TGG 0.335441 5.3:-13750816 None:intergenic
AGTTGGGTTGGTTTCTTTGA+GGG 0.364234 5.3:-13749933 None:intergenic
GGCTTCTTGATCGTCCTCTT+GGG 0.380085 5.3:-13750794 None:intergenic
GTCATGAGGGGACTTGTTGT+TGG 0.386730 5.3:-13749891 None:intergenic
TAGTTGGGTTGGTTTCTTTG+AGG 0.387471 5.3:-13749934 None:intergenic
TTGAATTCTCGGAAGGGTTA+GGG 0.403529 5.3:-13749862 None:intergenic
TCAGAGTCCTCTATCTCTAT+TGG 0.410192 5.3:-13750701 None:intergenic
AGGGGACTTGTTGTTGGTGG+GGG 0.410882 5.3:-13749885 None:intergenic
CTCTTGGGCCTTCCTTCCTC+TGG 0.410975 5.3:-13750779 None:intergenic
AAAGAACTCTGAAGGGTAGT+TGG 0.416606 5.3:-13749950 None:intergenic
TGAGGGGACTTGTTGTTGGT+GGG 0.418050 5.3:-13749887 None:intergenic
AAGAACTCTGAAGGGTAGTT+GGG 0.429468 5.3:-13749949 None:intergenic
CATGGTTATTCAGCACCTCC+TGG 0.431962 5.3:+13750142 MS.gene64862:CDS
TACAATGTCAAGTCAGGAAG+AGG 0.434728 5.3:+13750724 MS.gene64862:CDS
CAGTGTTGTTGTTTGCGCCT+TGG 0.435389 5.3:-13750754 None:intergenic
ACCTCAACCTGATCAATATG+AGG 0.437745 5.3:+13750201 MS.gene64862:CDS
AGGTGGGGTGGCTGTTGATG+TGG 0.445640 5.3:-13750182 None:intergenic
CCCTCATATTGATCAGGTTG+AGG 0.453934 5.3:-13750202 None:intergenic
GCAAACATGTGTTTCCCACT+TGG 0.463748 5.3:+13750071 MS.gene64862:CDS
AAGTGATGGTCAAGCTATGA+AGG 0.473835 5.3:+13750018 MS.gene64862:CDS
AAGCCAGCCAATAGAGATAG+AGG 0.474391 5.3:+13750694 MS.gene64862:CDS
GCTGTTGATGTGGAAGGAAG+TGG 0.478632 5.3:-13750172 None:intergenic
CTCTGATACAATGTCAAGTC+AGG 0.478904 5.3:+13750718 MS.gene64862:CDS
CATATTGATCAGGTTGAGGT+GGG 0.500892 5.3:-13750198 None:intergenic
AGTCCTCTATCTCTATTGGC+TGG 0.503791 5.3:-13750697 None:intergenic
ACTCTGAAGGGTAGTTGGGT+TGG 0.513668 5.3:-13749945 None:intergenic
CATCAGAGGGAGGGTCATGA+GGG 0.516551 5.3:-13749904 None:intergenic
AGCTCGTGAGAATGGGAAGC+TGG 0.517710 5.3:+13749976 MS.gene64862:CDS
CAAACATGTGTTTCCCACTT+GGG 0.531651 5.3:+13750072 MS.gene64862:CDS
GCTTATCAGTTGTATCGGCT+GGG 0.531837 5.3:-13750815 None:intergenic
TATATTTGTTGTCATCCTCA+TGG 0.532111 5.3:+13750124 MS.gene64862:CDS
TTGATCAGGTTGAGGTGGGG+TGG 0.544768 5.3:-13750194 None:intergenic
GAGGGGACTTGTTGTTGGTG+GGG 0.545536 5.3:-13749886 None:intergenic
TCATCAGAGGGAGGGTCATG+AGG 0.552597 5.3:-13749905 None:intergenic
TCATATTGATCAGGTTGAGG+TGG 0.558741 5.3:-13750199 None:intergenic
ACACTGGACCAGAGGAAGGA+AGG 0.561168 5.3:+13750771 MS.gene64862:CDS
TTTGAGGGATTCATCATCAG+AGG 0.561409 5.3:-13749918 None:intergenic
GAGCTGCTTATCAGTTGTAT+CGG 0.563493 5.3:-13750820 None:intergenic
GAGCTCTAAAAGAACTCTGA+AGG 0.563654 5.3:-13749958 None:intergenic
TTGAGGGATTCATCATCAGA+GGG 0.579951 5.3:-13749917 None:intergenic
CAAGGCGCAAACAACAACAC+TGG 0.583137 5.3:+13750755 MS.gene64862:CDS
AAACAACAACACTGGACCAG+AGG 0.583233 5.3:+13750763 MS.gene64862:CDS
CAGGAAGAGGGAAGGAACCA+AGG 0.586582 5.3:+13750737 MS.gene64862:CDS
GGGGTGGCTGTTGATGTGGA+AGG 0.586960 5.3:-13750178 None:intergenic
ATATTGATCAGGTTGAGGTG+GGG 0.595131 5.3:-13750197 None:intergenic
AACAACACTGGACCAGAGGA+AGG 0.595528 5.3:+13750767 MS.gene64862:CDS
CAGAGGAAGGAAGGCCCAAG+AGG 0.596615 5.3:+13750780 MS.gene64862:CDS
AGTGATGGTCAAGCTATGAA+GGG 0.603559 5.3:+13750019 MS.gene64862:CDS
AATGGGAAGCTGGCAGCTGA+TGG 0.610197 5.3:+13749986 MS.gene64862:CDS
AAGCTGGCAGCTGATGGCGA+AGG 0.613924 5.3:+13749992 MS.gene64862:CDS
AGCTCTAAAAGAACTCTGAA+GGG 0.619435 5.3:-13749957 None:intergenic
AGGGATTCATCATCAGAGGG+AGG 0.627786 5.3:-13749914 None:intergenic
CTTCATCAAAGTAGCCCAAG+TGG 0.635469 5.3:-13750086 None:intergenic
ATGGTCAAGCTATGAAGGGG+AGG 0.636182 5.3:+13750023 MS.gene64862:CDS
ACAATGTCAAGTCAGGAAGA+GGG 0.642713 5.3:+13750725 MS.gene64862:CDS
GGGATTCATCATCAGAGGGA+GGG 0.650027 5.3:-13749913 None:intergenic
CCTCAACCTGATCAATATGA+GGG 0.650750 5.3:+13750202 MS.gene64862:CDS
TTCATCAAAGTAGCCCAAGT+GGG 0.657037 5.3:-13750085 None:intergenic
TGTCAAGTCAGGAAGAGGGA+AGG 0.657401 5.3:+13750729 MS.gene64862:CDS
ATCAGAGGGAGGGTCATGAG+GGG 0.657979 5.3:-13749903 None:intergenic
GATGGCGAAGGAGTAAGTGA+TGG 0.658846 5.3:+13750004 MS.gene64862:CDS
GTGATGGTCAAGCTATGAAG+GGG 0.659294 5.3:+13750020 MS.gene64862:CDS
GGAGGTGCTGAATAACCATG+AGG 0.763451 5.3:-13750139 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AACATTAAATAATTGAATCT+TGG - chr5.3:13750353-13750372 None:intergenic 15.0%
!!! TTTTTCACACTATAATTTTT+AGG + chr5.3:13750283-13750302 MS.gene64862:intron 15.0%
!!! AATGTTTTTCTTTTGTTACT+AGG + chr5.3:13750662-13750681 MS.gene64862:intron 20.0%
!!! ACAATAAATAGTTTTGAGAT+AGG - chr5.3:13750247-13750266 None:intergenic 20.0%
! CATATATATGTTTGTGTCTA+TGG - chr5.3:13750478-13750497 None:intergenic 25.0%
! TTATGAGATCTAATTCATGT+AGG + chr5.3:13750521-13750540 MS.gene64862:intron 25.0%
!!! TAGTTTTGAGATAGGAAATT+AGG - chr5.3:13750239-13750258 None:intergenic 25.0%
GAATCTTGGACATGATATAT+AGG - chr5.3:13750339-13750358 None:intergenic 30.0%
TATATAGGCAATAAAACCCT+AGG - chr5.3:13750324-13750343 None:intergenic 30.0%
!! TATATTTGTTGTCATCCTCA+TGG + chr5.3:13750124-13750143 MS.gene64862:CDS 30.0%
! GTTTTACCCTCATATTGATC+AGG - chr5.3:13750211-13750230 None:intergenic 35.0%
!! AGCTCTAAAAGAACTCTGAA+GGG - chr5.3:13749960-13749979 None:intergenic 35.0%
AAGTGATGGTCAAGCTATGA+AGG + chr5.3:13750018-13750037 MS.gene64862:CDS 40.0%
ACAATGTCAAGTCAGGAAGA+GGG + chr5.3:13750725-13750744 MS.gene64862:CDS 40.0%
ACCTCAACCTGATCAATATG+AGG + chr5.3:13750201-13750220 MS.gene64862:CDS 40.0%
AGTGATGGTCAAGCTATGAA+GGG + chr5.3:13750019-13750038 MS.gene64862:CDS 40.0%
CAAACATGTGTTTCCCACTT+GGG + chr5.3:13750072-13750091 MS.gene64862:CDS 40.0%
CCTCAACCTGATCAATATGA+GGG + chr5.3:13750202-13750221 MS.gene64862:CDS 40.0%
CTCTGATACAATGTCAAGTC+AGG + chr5.3:13750718-13750737 MS.gene64862:CDS 40.0%
TACAATGTCAAGTCAGGAAG+AGG + chr5.3:13750724-13750743 MS.gene64862:CDS 40.0%
TCAGAGTCCTCTATCTCTAT+TGG - chr5.3:13750704-13750723 None:intergenic 40.0%
TTCATCAAAGTAGCCCAAGT+GGG - chr5.3:13750088-13750107 None:intergenic 40.0%
TTGAATTCTCGGAAGGGTTA+GGG - chr5.3:13749865-13749884 None:intergenic 40.0%
TTGAGGGATTCATCATCAGA+GGG - chr5.3:13749920-13749939 None:intergenic 40.0%
TTTGAGGGATTCATCATCAG+AGG - chr5.3:13749921-13749940 None:intergenic 40.0%
! AAAGAACTCTGAAGGGTAGT+TGG - chr5.3:13749953-13749972 None:intergenic 40.0%
! AAGAACTCTGAAGGGTAGTT+GGG - chr5.3:13749952-13749971 None:intergenic 40.0%
!! AGTTGGGTTGGTTTCTTTGA+GGG - chr5.3:13749936-13749955 None:intergenic 40.0%
!! ATATTGATCAGGTTGAGGTG+GGG - chr5.3:13750200-13750219 None:intergenic 40.0%
!! CATATTGATCAGGTTGAGGT+GGG - chr5.3:13750201-13750220 None:intergenic 40.0%
!! GAGCTCTAAAAGAACTCTGA+AGG - chr5.3:13749961-13749980 None:intergenic 40.0%
!! TAGTTGGGTTGGTTTCTTTG+AGG - chr5.3:13749937-13749956 None:intergenic 40.0%
!! TCATATTGATCAGGTTGAGG+TGG - chr5.3:13750202-13750221 None:intergenic 40.0%
!!! CTTTTAGAGCTCGTGAGAAT+GGG + chr5.3:13749969-13749988 MS.gene64862:CDS 40.0%
!!! TCTTTTAGAGCTCGTGAGAA+TGG + chr5.3:13749968-13749987 MS.gene64862:CDS 40.0%
AAACAACAACACTGGACCAG+AGG + chr5.3:13750763-13750782 MS.gene64862:CDS 45.0%
AAGCCAGCCAATAGAGATAG+AGG + chr5.3:13750694-13750713 MS.gene64862:CDS 45.0%
AGTCCTCTATCTCTATTGGC+TGG - chr5.3:13750700-13750719 None:intergenic 45.0%
CTTCATCAAAGTAGCCCAAG+TGG - chr5.3:13750089-13750108 None:intergenic 45.0%
GAAGGAAGTGGAGAAAAACC+AGG - chr5.3:13750163-13750182 None:intergenic 45.0%
GCAAACATGTGTTTCCCACT+TGG + chr5.3:13750071-13750090 MS.gene64862:CDS 45.0%
GCAATAAAACCCTAGGTCAC+TGG - chr5.3:13750317-13750336 None:intergenic 45.0%
GTGATGGTCAAGCTATGAAG+GGG + chr5.3:13750020-13750039 MS.gene64862:CDS 45.0%
GTTGAATTCTCGGAAGGGTT+AGG - chr5.3:13749866-13749885 None:intergenic 45.0%
! CCCTCATATTGATCAGGTTG+AGG - chr5.3:13750205-13750224 None:intergenic 45.0%
!!! TAATTTTTTATATAACTTAT+TGG + chr5.3:13750562-13750581 MS.gene64862:intron 5.0%
AACAACACTGGACCAGAGGA+AGG + chr5.3:13750767-13750786 MS.gene64862:CDS 50.0%
AGGGATTCATCATCAGAGGG+AGG - chr5.3:13749917-13749936 None:intergenic 50.0%
ATGGTCAAGCTATGAAGGGG+AGG + chr5.3:13750023-13750042 MS.gene64862:CDS 50.0%
CAAGGCGCAAACAACAACAC+TGG + chr5.3:13750755-13750774 MS.gene64862:CDS 50.0%
CATGGTTATTCAGCACCTCC+TGG + chr5.3:13750142-13750161 MS.gene64862:CDS 50.0%
GATGGCGAAGGAGTAAGTGA+TGG + chr5.3:13750004-13750023 MS.gene64862:CDS 50.0%
GCTGTTGATGTGGAAGGAAG+TGG - chr5.3:13750175-13750194 None:intergenic 50.0%
GGAAGTGGAGAAAAACCAGG+AGG - chr5.3:13750160-13750179 None:intergenic 50.0%
GGCTTCTTGATCGTCCTCTT+GGG - chr5.3:13750797-13750816 None:intergenic 50.0%
GGGATTCATCATCAGAGGGA+GGG - chr5.3:13749916-13749935 None:intergenic 50.0%
GTCAACACTCCAGTGACCTA+GGG + chr5.3:13750305-13750324 MS.gene64862:intron 50.0%
TGGGGGTTGAATTCTCGGAA+GGG - chr5.3:13749871-13749890 None:intergenic 50.0%
TGTCAAGTCAGGAAGAGGGA+AGG + chr5.3:13750729-13750748 MS.gene64862:CDS 50.0%
! ACTCTGAAGGGTAGTTGGGT+TGG - chr5.3:13749948-13749967 None:intergenic 50.0%
! GTTGGTGGGGGTTGAATTCT+CGG - chr5.3:13749876-13749895 None:intergenic 50.0%
!! ATGAGGGGACTTGTTGTTGG+TGG - chr5.3:13749891-13749910 None:intergenic 50.0%
!! CAGTGTTGTTGTTTGCGCCT+TGG - chr5.3:13750757-13750776 None:intergenic 50.0%
!! GGAGGTGCTGAATAACCATG+AGG - chr5.3:13750142-13750161 None:intergenic 50.0%
!! GTCATGAGGGGACTTGTTGT+TGG - chr5.3:13749894-13749913 None:intergenic 50.0%
!! TGAGGGGACTTGTTGTTGGT+GGG - chr5.3:13749890-13749909 None:intergenic 50.0%
AATGGGAAGCTGGCAGCTGA+TGG + chr5.3:13749986-13750005 MS.gene64862:CDS 55.0%
ACACTGGACCAGAGGAAGGA+AGG + chr5.3:13750771-13750790 MS.gene64862:CDS 55.0%
AGCTCGTGAGAATGGGAAGC+TGG + chr5.3:13749976-13749995 MS.gene64862:CDS 55.0%
ATCAGAGGGAGGGTCATGAG+GGG - chr5.3:13749906-13749925 None:intergenic 55.0%
CAGGAAGAGGGAAGGAACCA+AGG + chr5.3:13750737-13750756 MS.gene64862:CDS 55.0%
CATCAGAGGGAGGGTCATGA+GGG - chr5.3:13749907-13749926 None:intergenic 55.0%
GGGCTTCTTGATCGTCCTCT+TGG - chr5.3:13750798-13750817 None:intergenic 55.0%
GGTCAACACTCCAGTGACCT+AGG + chr5.3:13750304-13750323 MS.gene64862:intron 55.0%
GTGGGGGTTGAATTCTCGGA+AGG - chr5.3:13749872-13749891 None:intergenic 55.0%
TCATCAGAGGGAGGGTCATG+AGG - chr5.3:13749908-13749927 None:intergenic 55.0%
!! AGGGGACTTGTTGTTGGTGG+GGG - chr5.3:13749888-13749907 None:intergenic 55.0%
!! GAGGGGACTTGTTGTTGGTG+GGG - chr5.3:13749889-13749908 None:intergenic 55.0%
!! TTGATCAGGTTGAGGTGGGG+TGG - chr5.3:13750197-13750216 None:intergenic 55.0%
AGGTGGGGTGGCTGTTGATG+TGG - chr5.3:13750185-13750204 None:intergenic 60.0%
CAGAGGAAGGAAGGCCCAAG+AGG + chr5.3:13750780-13750799 MS.gene64862:CDS 60.0%
CTCTTGGGCCTTCCTTCCTC+TGG - chr5.3:13750782-13750801 None:intergenic 60.0%
GGGGTGGCTGTTGATGTGGA+AGG - chr5.3:13750181-13750200 None:intergenic 60.0%
! AAGCTGGCAGCTGATGGCGA+AGG + chr5.3:13749992-13750011 MS.gene64862:CDS 60.0%


Chromosome Type Strat End Strand Name
chr5.3 gene 13749854 13750832 13749854 ID=MS.gene64862
chr5.3 mRNA 13749854 13750832 13749854 ID=MS.gene64862.t1;Parent=MS.gene64862
chr5.3 exon 13749854 13750223 13749854 ID=MS.gene64862.t1.exon1;Parent=MS.gene64862.t1
chr5.3 CDS 13749854 13750223 13749854 ID=cds.MS.gene64862.t1;Parent=MS.gene64862.t1
chr5.3 exon 13750684 13750832 13750684 ID=MS.gene64862.t1.exon2;Parent=MS.gene64862.t1
chr5.3 CDS 13750684 13750832 13750684 ID=cds.MS.gene64862.t1;Parent=MS.gene64862.t1
Gene Sequence

>MS.gene64862

ATGCAGAACCCTAACCCTTCCGAGAATTCAACCCCCACCAACAACAAGTCCCCTCATGACCCTCCCTCTGATGATGAATCCCTCAAAGAAACCAACCCAACTACCCTTCAGAGTTCTTTTAGAGCTCGTGAGAATGGGAAGCTGGCAGCTGATGGCGAAGGAGTAAGTGATGGTCAAGCTATGAAGGGGAGGAAGAGTAATATTTGTTGTCATAGATGCAAACATGTGTTTCCCACTTGGGCTACTTTGATGAAGCATTATCAAGAACACTATATTTGTTGTCATCCTCATGGTTATTCAGCACCTCCTGGTTTTTCTCCACTTCCTTCCACATCAACAGCCACCCCACCTCAACCTGATCAATATGAGGGTAAAACTAAAACCTAATTTCCTATCTCAAAACTATTTATTGTCATGTCTTTTTTTTTTTTTTTCACACTATAATTTTTAGGTCAACACTCCAGTGACCTAGGGTTTTATTGCCTATATATCATGTCCAAGATTCAATTATTTAATGTTATATAATTATTATTTTTTTCATTTAATTATTTTGATTTCAAAGTACTTGTGTATAGATCATTCATAAAATACTTGTGTATAGATCATTCATAAAAGATTGCACCATAGACACAAACATATATATGTTCACTTTGAGTGTTGCTTAATTTTATGAGATCTAATTCATGTAGGCATCTATATATATATCTTTAATTTTTTATATAACTTATTGGTTTTTAATTTAACAATTTGTTTTTTTTTTCTTTCAAACTAATGATTTTACAATGAAGCAATTATAATTATAATTTTGAATGTTTTTCTTTTGTTACTAGGTGATGATCAAAGCCAGCCAATAGAGATAGAGGACTCTGATACAATGTCAAGTCAGGAAGAGGGAAGGAACCAAGGCGCAAACAACAACACTGGACCAGAGGAAGGAAGGCCCAAGAGGACGATCAAGAAGCCCAGCCGATACAACTGA
Protein sequence

>MS.gene64862.t1

MQNPNPSENSTPTNNKSPHDPPSDDESLKETNPTTLQSSFRARENGKLAADGEGVSDGQAMKGRKSNICCHRCKHVFPTWATLMKHYQEHYICCHPHGYSAPPGFSPLPSTSTATPPQPDQYEGDDQSQPIEIEDSDTMSSQEEGRNQGANNNTGPEEGRPKRTIKKPSRYN