AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar ZhongmuNo.1 / MsG0180005590.01

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0180005590.01.T01 MTR_1g103420 94.643 224 5 1 1 224 1 217 1.16e-142 397
MsG0180005590.01.T01 MTR_5g006940 57.143 224 84 5 1 224 1 212 3.99e-68 208
MsG0180005590.01.T01 MTR_1g071720 55.660 106 43 4 26 128 26 130 3.06e-31 113
MsG0180005590.01.T01 MTR_1g071720 55.660 106 43 4 26 128 26 130 3.29e-31 113
MsG0180005590.01.T01 MTR_7g095250 48.544 103 46 3 37 132 2 104 9.96e-23 91.3
MsG0180005590.01.T01 MTR_1g103450 33.636 110 65 4 10 118 8 110 9.03e-11 58.5
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0180005590.01.T01 AT1G05450 60.993 141 48 3 26 166 27 160 1.88e-46 153
MsG0180005590.01.T01 AT3G22620 45.622 217 94 7 10 224 9 203 1.39e-42 143
MsG0180005590.01.T01 AT2G48140 48.428 159 70 6 12 159 7 164 2.57e-36 127
MsG0180005590.01.T01 AT2G48140 53.913 115 51 2 12 125 7 120 2.33e-35 122

Find 71 sgRNAs with CRISPR-Local

Find 88 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CACTCTCTTCACACCTTGTA+TGG 0.248146 1:-93728841 MsG0180005590.01.T01:CDS
AATCCATGCCACTACTTGTT+AGG 0.277189 1:+93728751 None:intergenic
AAGAGAGTGCTTATTGTAGA+AGG 0.288971 1:+93728855 None:intergenic
GGAGATGAAGTTGGTGAAGC+TGG 0.347569 1:+93728004 None:intergenic
ATAGCTAAGGTTCTATTGAT+TGG 0.350447 1:+93728687 None:intergenic
CTTACAGGTAGTAGTGCTAA+TGG 0.358055 1:-93728813 MsG0180005590.01.T01:CDS
GTCATTAATATTGTCATGGC+TGG 0.381229 1:-93728912 MsG0180005590.01.T01:CDS
CCATCGCCCTCGGTGAATTC+CGG 0.383644 1:-93727938 MsG0180005590.01.T01:CDS
CTTCCAGTTGTCGATGTAGA+TGG 0.386358 1:+93727911 None:intergenic
TACTGTTCTATTGATTGCAC+TGG 0.398561 1:-93727834 MsG0180005590.01.T01:CDS
GAGATGAAGTTGGTGAAGCT+GGG 0.416122 1:+93728005 None:intergenic
TGCTAATAACCTTGAGGACT+AGG 0.423773 1:+93728150 None:intergenic
CTTATTGTAGAAGGGTTACA+TGG 0.446986 1:+93728864 None:intergenic
TCACCTGCATCTTCTCCCTC+AGG 0.449806 1:-93728186 MsG0180005590.01.T01:CDS
ATCCATGCCACTACTTGTTA+GGG 0.450316 1:+93728752 None:intergenic
TGGGGTGTTGATTTGTGCAT+TGG 0.461296 1:+93728884 None:intergenic
TGAGACATTGTAAGATGTAA+TGG 0.469321 1:+93727859 None:intergenic
GCTAATAACCTTGAGGACTA+GGG 0.472496 1:+93728151 None:intergenic
TTTGACTCCGCCATCGCCCT+CGG 0.482556 1:-93727948 MsG0180005590.01.T01:CDS
TTCACCAACTTCATCTCCTC+TGG 0.485231 1:-93727999 MsG0180005590.01.T01:CDS
CCTCGTGCTTGTAACATGCC+TGG 0.487865 1:-93728657 MsG0180005590.01.T01:CDS
ATTCCATCTACATCGACAAC+TGG 0.490256 1:-93727914 MsG0180005590.01.T01:CDS
ATGTCACCTAGCAATAATAT+TGG 0.492160 1:-93728934 MsG0180005590.01.T01:CDS
GCTTCACCACTTCCTGCTCC+TGG 0.495227 1:-93728489 MsG0180005590.01.T01:intron
GCATTACCAGGAGCAGGAAG+TGG 0.522233 1:+93728483 None:intergenic
AGAGAGTGCTTATTGTAGAA+GGG 0.525567 1:+93728856 None:intergenic
TAATGACCAATATTATTGCT+AGG 0.532925 1:+93728928 None:intergenic
AATCCTGAGGGAGAAGATGC+AGG 0.533311 1:+93728183 None:intergenic
AGCAGGAAGTGGTGAAGCTG+AGG 0.535400 1:+93728494 None:intergenic
CCGGAATTCACCGAGGGCGA+TGG 0.539092 1:+93727938 None:intergenic
ATTCCAACCCCTAGTCCTCA+AGG 0.540237 1:-93728159 MsG0180005590.01.T01:intron
ACTCTCTTCACACCTTGTAT+GGG 0.540459 1:-93728840 MsG0180005590.01.T01:CDS
AATTTGGCATTACCAGGAGC+AGG 0.546347 1:+93728477 None:intergenic
TTCACAGGTCCTGTGGCTCT+AGG 0.546401 1:-93728219 MsG0180005590.01.T01:intron
TAACCTTGAGGACTAGGGGT+TGG 0.546635 1:+93728156 None:intergenic
ATGTATATTCACAGGTCCTG+TGG 0.548141 1:-93728226 MsG0180005590.01.T01:intron
ATCCCTAACAAGTAGTGGCA+TGG 0.551127 1:-93728754 MsG0180005590.01.T01:CDS
CTTAAATCCCTAACAAGTAG+TGG 0.551269 1:-93728759 MsG0180005590.01.T01:CDS
ATTGGTCATTAATATTGTCA+TGG 0.553363 1:-93728916 MsG0180005590.01.T01:CDS
TGTCGATGTAGATGGAATAC+CGG 0.553646 1:+93727919 None:intergenic
TGAGATGGTCCTAGAGCCAC+AGG 0.556902 1:+93728210 None:intergenic
ACTGTTCTATTGATTGCACT+GGG 0.566423 1:-93727833 MsG0180005590.01.T01:CDS
CCTGTAAGAAAACCCATACA+AGG 0.567820 1:+93728828 None:intergenic
GGAACATTTGTGTCTTGTTG+TGG 0.568188 1:+93727974 None:intergenic
TAAGATGTAATGGCAGATGA+TGG 0.568483 1:+93727869 None:intergenic
TTGCATTGAACTGGAACACC+AGG 0.568933 1:+93728639 None:intergenic
GGCGATGGCGGAGTCAAAAG+AGG 0.572662 1:+93727953 None:intergenic
AAGAGCACCGCAACATTCAG+TGG 0.581316 1:+93728779 None:intergenic
AGGGAACACTAGCAGTTACA+AGG 0.586483 1:+93728718 None:intergenic
AGTGCAATCAATAGAACAGT+AGG 0.586789 1:+93727836 None:intergenic
GTGTCTTGTTGTGGTGCCAG+AGG 0.590812 1:+93727983 None:intergenic
GCACCGCAACATTCAGTGGT+TGG 0.593515 1:+93728783 None:intergenic
TCTACATCGACAACTGGAAG+CGG 0.603015 1:-93727908 MsG0180005590.01.T01:CDS
GAAGATGCAGGTGAATGAGA+TGG 0.607870 1:+93728195 None:intergenic
GAATTCACCGAGGGCGATGG+CGG 0.615597 1:+93727941 None:intergenic
GGTGTTCCAGTTCAATGCAA+AGG 0.630148 1:-93728636 MsG0180005590.01.T01:intron
CCAGGCATGTTACAAGCACG+AGG 0.631598 1:+93728657 None:intergenic
TGGTGAAGCTGGGAGGTCAG+AGG 0.633468 1:+93728015 None:intergenic
ACGAGGGAGAGAGATAGCTA+AGG 0.635982 1:+93728674 None:intergenic
CTAATAACCTTGAGGACTAG+GGG 0.642081 1:+93728152 None:intergenic
TCACCAACCACTGAATGTTG+CGG 0.642405 1:-93728786 MsG0180005590.01.T01:CDS
TTATTGTAGAAGGGTTACAT+GGG 0.644859 1:+93728865 None:intergenic
GCAACATTCAGTGGTTGGTG+AGG 0.651267 1:+93728788 None:intergenic
GGGGTTGGAATAAATCCTGA+GGG 0.662198 1:+93728171 None:intergenic
AGGGGTTGGAATAAATCCTG+AGG 0.672890 1:+93728170 None:intergenic
GGTGCCAGAGGAGATGAAGT+TGG 0.674504 1:+93727995 None:intergenic
GGAATACCGGAATTCACCGA+GGG 0.686162 1:+93727932 None:intergenic
TATTGTAGAAGGGTTACATG+GGG 0.692481 1:+93728866 None:intergenic
ATGAAGTTGGTGAAGCTGGG+AGG 0.696977 1:+93728008 None:intergenic
TGGAATACCGGAATTCACCG+AGG 0.697163 1:+93727931 None:intergenic
CAGGCATGTTACAAGCACGA+GGG 0.748196 1:+93728658 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAATTATTGGAATTGAAATT+TGG + Chr1:93728304-93728323 None:intergenic 15.0%
!! AATTTGTGTACAAAAATTAT+TGG + Chr1:93728317-93728336 None:intergenic 15.0%
!! CATTATTAAGATTAATTCAA+AGG + Chr1:93728510-93728529 None:intergenic 15.0%
!!! GTTAGAAAATATTTTTGTTA+GGG + Chr1:93728362-93728381 None:intergenic 15.0%
!!! TGTTAGAAAATATTTTTGTT+AGG + Chr1:93728363-93728382 None:intergenic 15.0%
! ATTGGTCATTAATATTGTCA+TGG - Chr1:93727846-93727865 MsG0180005590.01.T01:CDS 25.0%
! TAATGACCAATATTATTGCT+AGG + Chr1:93727837-93727856 None:intergenic 25.0%
! TCAAAGAAAAATGTAAGAGT+TGG + Chr1:93728720-93728739 None:intergenic 25.0%
! TCAAAGGAAAAATAGTTTAG+AGG + Chr1:93728494-93728513 None:intergenic 25.0%
!! TTTTGTTAGGGATTATAGAA+GGG + Chr1:93728350-93728369 None:intergenic 25.0%
!! TTTTTGTTAGGGATTATAGA+AGG + Chr1:93728351-93728370 None:intergenic 25.0%
!!! CTATTGATTGGAATTTTGAA+GGG + Chr1:93728066-93728085 None:intergenic 25.0%
!!! TCTATTGATTGGAATTTTGA+AGG + Chr1:93728067-93728086 None:intergenic 25.0%
!!! TGATTTTGATGTATATTCAC+AGG - Chr1:93728528-93728547 MsG0180005590.01.T01:intron 25.0%
AATTGAAATTTGGCATTACC+AGG + Chr1:93728294-93728313 None:intergenic 30.0%
ATAGCTAAGGTTCTATTGAT+TGG + Chr1:93728078-93728097 None:intergenic 30.0%
ATGTCACCTAGCAATAATAT+TGG - Chr1:93727828-93727847 MsG0180005590.01.T01:CDS 30.0%
CTATCATCTAGTAACATTGT+AGG - Chr1:93728461-93728480 MsG0180005590.01.T01:intron 30.0%
TGAGACATTGTAAGATGTAA+TGG + Chr1:93728906-93728925 None:intergenic 30.0%
TTATTGTAGAAGGGTTACAT+GGG + Chr1:93727900-93727919 None:intergenic 30.0%
! TTTTTACCTTTGCATTGAAC+TGG + Chr1:93728135-93728154 None:intergenic 30.0%
AGTGCAATCAATAGAACAGT+AGG + Chr1:93728929-93728948 None:intergenic 35.0%
CTTAAATCCCTAACAAGTAG+TGG - Chr1:93728003-93728022 MsG0180005590.01.T01:CDS 35.0%
CTTATTGTAGAAGGGTTACA+TGG + Chr1:93727901-93727920 None:intergenic 35.0%
GTCATTAATATTGTCATGGC+TGG - Chr1:93727850-93727869 MsG0180005590.01.T01:CDS 35.0%
GTGTAATGCTAATAACCTTG+AGG + Chr1:93728621-93728640 None:intergenic 35.0%
TAAGATGTAATGGCAGATGA+TGG + Chr1:93728896-93728915 None:intergenic 35.0%
TATTGTAGAAGGGTTACATG+GGG + Chr1:93727899-93727918 None:intergenic 35.0%
! ACTGTTCTATTGATTGCACT+GGG - Chr1:93728929-93728948 MsG0180005590.01.T01:CDS 35.0%
! TACTGTTCTATTGATTGCAC+TGG - Chr1:93728928-93728947 MsG0180005590.01.T01:CDS 35.0%
!! AAGAGAGTGCTTATTGTAGA+AGG + Chr1:93727910-93727929 None:intergenic 35.0%
!! AGAGAGTGCTTATTGTAGAA+GGG + Chr1:93727909-93727928 None:intergenic 35.0%
AATCCATGCCACTACTTGTT+AGG + Chr1:93728014-93728033 None:intergenic 40.0%
ACTCTCTTCACACCTTGTAT+GGG - Chr1:93727922-93727941 MsG0180005590.01.T01:CDS 40.0%
ATGTATATTCACAGGTCCTG+TGG - Chr1:93728536-93728555 MsG0180005590.01.T01:intron 40.0%
ATTCCATCTACATCGACAAC+TGG - Chr1:93728848-93728867 MsG0180005590.01.T01:CDS 40.0%
CCTGTAAGAAAACCCATACA+AGG + Chr1:93727937-93727956 None:intergenic 40.0%
CTAATAACCTTGAGGACTAG+GGG + Chr1:93728613-93728632 None:intergenic 40.0%
CTTACAGGTAGTAGTGCTAA+TGG - Chr1:93727949-93727968 MsG0180005590.01.T01:CDS 40.0%
GCTAATAACCTTGAGGACTA+GGG + Chr1:93728614-93728633 None:intergenic 40.0%
TGCTAATAACCTTGAGGACT+AGG + Chr1:93728615-93728634 None:intergenic 40.0%
TGTCGATGTAGATGGAATAC+CGG + Chr1:93728846-93728865 None:intergenic 40.0%
! ATCCATGCCACTACTTGTTA+GGG + Chr1:93728013-93728032 None:intergenic 40.0%
! CCTTGTATGGGTTTTCTTAC+AGG - Chr1:93727934-93727953 MsG0180005590.01.T01:CDS 40.0%
! GGAACATTTGTGTCTTGTTG+TGG + Chr1:93728791-93728810 None:intergenic 40.0%
AATTTGGCATTACCAGGAGC+AGG + Chr1:93728288-93728307 None:intergenic 45.0%
AGGGAACACTAGCAGTTACA+AGG + Chr1:93728047-93728066 None:intergenic 45.0%
AGGGGTTGGAATAAATCCTG+AGG + Chr1:93728595-93728614 None:intergenic 45.0%
ATCCCTAACAAGTAGTGGCA+TGG - Chr1:93728008-93728027 MsG0180005590.01.T01:CDS 45.0%
CACTCTCTTCACACCTTGTA+TGG - Chr1:93727921-93727940 MsG0180005590.01.T01:CDS 45.0%
CTTCCAGTTGTCGATGTAGA+TGG + Chr1:93728854-93728873 None:intergenic 45.0%
GAAGATGCAGGTGAATGAGA+TGG + Chr1:93728570-93728589 None:intergenic 45.0%
GGGGTTGGAATAAATCCTGA+GGG + Chr1:93728594-93728613 None:intergenic 45.0%
GGTGTTCCAGTTCAATGCAA+AGG - Chr1:93728126-93728145 MsG0180005590.01.T01:intron 45.0%
TCACCAACCACTGAATGTTG+CGG - Chr1:93727976-93727995 MsG0180005590.01.T01:CDS 45.0%
TCTACATCGACAACTGGAAG+CGG - Chr1:93728854-93728873 MsG0180005590.01.T01:CDS 45.0%
TTCACCAACTTCATCTCCTC+TGG - Chr1:93728763-93728782 MsG0180005590.01.T01:CDS 45.0%
TTGCATTGAACTGGAACACC+AGG + Chr1:93728126-93728145 None:intergenic 45.0%
!! GAGATGAAGTTGGTGAAGCT+GGG + Chr1:93728760-93728779 None:intergenic 45.0%
!! TGGGGTGTTGATTTGTGCAT+TGG + Chr1:93727881-93727900 None:intergenic 45.0%
AATCCTGAGGGAGAAGATGC+AGG + Chr1:93728582-93728601 None:intergenic 50.0%
ACGAGGGAGAGAGATAGCTA+AGG + Chr1:93728091-93728110 None:intergenic 50.0%
ATTCCAACCCCTAGTCCTCA+AGG - Chr1:93728603-93728622 MsG0180005590.01.T01:intron 50.0%
CAGGCATGTTACAAGCACGA+GGG + Chr1:93728107-93728126 None:intergenic 50.0%
GGAATACCGGAATTCACCGA+GGG + Chr1:93728833-93728852 None:intergenic 50.0%
TAACCTTGAGGACTAGGGGT+TGG + Chr1:93728609-93728628 None:intergenic 50.0%
TGGAATACCGGAATTCACCG+AGG + Chr1:93728834-93728853 None:intergenic 50.0%
! GCAACATTCAGTGGTTGGTG+AGG + Chr1:93727977-93727996 None:intergenic 50.0%
!! AAGAGCACCGCAACATTCAG+TGG + Chr1:93727986-93728005 None:intergenic 50.0%
!! ATGAAGTTGGTGAAGCTGGG+AGG + Chr1:93728757-93728776 None:intergenic 50.0%
!! GGAGATGAAGTTGGTGAAGC+TGG + Chr1:93728761-93728780 None:intergenic 50.0%
AGCAGGAAGTGGTGAAGCTG+AGG + Chr1:93728271-93728290 None:intergenic 55.0%
CCAGGCATGTTACAAGCACG+AGG + Chr1:93728108-93728127 None:intergenic 55.0%
CCTCGTGCTTGTAACATGCC+TGG - Chr1:93728105-93728124 MsG0180005590.01.T01:intron 55.0%
GCACCGCAACATTCAGTGGT+TGG + Chr1:93727982-93728001 None:intergenic 55.0%
GCATTACCAGGAGCAGGAAG+TGG + Chr1:93728282-93728301 None:intergenic 55.0%
GGTGCCAGAGGAGATGAAGT+TGG + Chr1:93728770-93728789 None:intergenic 55.0%
TCACCTGCATCTTCTCCCTC+AGG - Chr1:93728576-93728595 MsG0180005590.01.T01:intron 55.0%
TGAGATGGTCCTAGAGCCAC+AGG + Chr1:93728555-93728574 None:intergenic 55.0%
TTCACAGGTCCTGTGGCTCT+AGG - Chr1:93728543-93728562 MsG0180005590.01.T01:intron 55.0%
! GTGTCTTGTTGTGGTGCCAG+AGG + Chr1:93728782-93728801 None:intergenic 55.0%
CCATCGCCCTCGGTGAATTC+CGG - Chr1:93728824-93728843 MsG0180005590.01.T01:CDS 60.0%
GAATTCACCGAGGGCGATGG+CGG + Chr1:93728824-93728843 None:intergenic 60.0%
GCTTCACCACTTCCTGCTCC+TGG - Chr1:93728273-93728292 MsG0180005590.01.T01:intron 60.0%
TGGTGAAGCTGGGAGGTCAG+AGG + Chr1:93728750-93728769 None:intergenic 60.0%
TTTGACTCCGCCATCGCCCT+CGG - Chr1:93728814-93728833 MsG0180005590.01.T01:CDS 60.0%
!! GGCGATGGCGGAGTCAAAAG+AGG + Chr1:93728812-93728831 None:intergenic 60.0%
CCGGAATTCACCGAGGGCGA+TGG + Chr1:93728827-93728846 None:intergenic 65.0%
Chromosome Type Strat End Strand Name
Chr1 gene 93727808 93728976 93727808 ID=MsG0180005590.01;Name=MsG0180005590.01
Chr1 mRNA 93727808 93728976 93727808 ID=MsG0180005590.01.T01;Parent=MsG0180005590.01;Name=MsG0180005590.01.T01;_AED=0.49;_eAED=0.50;_QI=0|0|0|1|1|1|4|0|224
Chr1 exon 93728637 93728976 93728637 ID=MsG0180005590.01.T01:exon:49896;Parent=MsG0180005590.01.T01
Chr1 exon 93728490 93728516 93728490 ID=MsG0180005590.01.T01:exon:49895;Parent=MsG0180005590.01.T01
Chr1 exon 93728160 93728234 93728160 ID=MsG0180005590.01.T01:exon:49894;Parent=MsG0180005590.01.T01
Chr1 exon 93727808 93728040 93727808 ID=MsG0180005590.01.T01:exon:49893;Parent=MsG0180005590.01.T01
Chr1 CDS 93728637 93728976 93728637 ID=MsG0180005590.01.T01:cds;Parent=MsG0180005590.01.T01
Chr1 CDS 93728490 93728516 93728490 ID=MsG0180005590.01.T01:cds;Parent=MsG0180005590.01.T01
Chr1 CDS 93728160 93728234 93728160 ID=MsG0180005590.01.T01:cds;Parent=MsG0180005590.01.T01
Chr1 CDS 93727808 93728040 93727808 ID=MsG0180005590.01.T01:cds;Parent=MsG0180005590.01.T01
Gene Sequence

>MsG0180005590.01.T01

ATGGCAAATTATGCTACTCTATGTCACCTAGCAATAATATTGGTCATTAATATTGTCATGGCTGGACAAGCCAATGCACAAATCAACACCCCATGTAACCCTTCTACAATAAGCACTCTCTTCACACCTTGTATGGGTTTTCTTACAGGTAGTAGTGCTAATGGCACCTCACCAACCACTGAATGTTGCGGTGCTCTTAAATCCCTAACAAGTAGTGGCATGGATTGTTTGTGTCTCCTTGTAACTGCTAGTGTTCCCTTCAAAATTCCAATCAATAGAACCTTAGCTATCTCTCTCCCTCGTGCTTGTAACATGCCTGGTGTTCCAGTTCAATGCAAAGCCTCAGCTTCACCACTTCCTGCTCCTGGTCCTGTGGCTCTAGGACCATCTCATTCACCTGCATCTTCTCCCTCAGGATTTATTCCAACCCCTAGTCCTCAAGCATCCTCTGACCTCCCAGCTTCACCAACTTCATCTCCTCTGGCACCACAACAAGACACAAATGTTCCTCTTTTGACTCCGCCATCGCCCTCGGTGAATTCCGGTATTCCATCTACATCGACAACTGGAAGCGGTCGCTCTTCTCTGACTCCATCATCTGCCATTACATCTTACAATGTCTCACCTACTGTTCTATTGATTGCACTGGGATTTGTTGCTCTCAAATACTACTAG
Protein sequence

>MsG0180005590.01.T01

MANYATLCHLAIILVINIVMAGQANAQINTPCNPSTISTLFTPCMGFLTGSSANGTSPTTECCGALKSLTSSGMDCLCLLVTASVPFKIPINRTLAISLPRACNMPGVPVQCKASASPLPAPGPVALGPSHSPASSPSGFIPTPSPQASSDLPASPTSSPLAPQQDTNVPLLTPPSPSVNSGIPSTSTTGSGRSSLTPSSAITSYNVSPTVLLIALGFVALKYY*