AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0893840


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0893840 MtrunA17_Chr6g0476821 80.597 134 25 1 80 212 13 146 5.46e-72 215
Msa0893840 MtrunA17_Chr6g0476921 52.727 220 87 10 1 212 1 211 6.27e-54 171
Msa0893840 MtrunA17_Chr6g0467611 42.727 220 115 8 1 212 1 217 3.86e-42 142
Msa0893840 MtrunA17_Chr6g0467761 42.727 220 115 8 1 212 1 217 6.99e-42 141
Msa0893840 MtrunA17_Chr6g0467621 42.202 218 115 8 1 210 1 215 2.64e-41 139
Msa0893840 MtrunA17_Chr6g0476961 45.070 213 98 9 1 207 1 200 9.68e-40 135
Msa0893840 MtrunA17_Chr6g0467771 41.364 220 117 9 1 212 1 216 1.03e-39 135
Msa0893840 MtrunA17_Chr6g0476951 45.327 214 97 10 1 207 1 201 6.04e-39 133
Msa0893840 MtrunA17_Chr6g0477281 39.130 207 93 7 1 201 1 180 7.42e-31 111
Msa0893840 MtrunA17_Chr3g0104591 40.415 193 100 9 25 207 22 209 3.30e-30 110
Msa0893840 MtrunA17_Chr6g0477741 39.367 221 114 12 1 211 1 211 3.25e-28 105
Msa0893840 MtrunA17_Chr6g0452491 39.151 212 110 11 1 202 1 203 1.03e-25 99.4
Msa0893840 MtrunA17_Chr6g0476831 36.842 209 119 7 1 201 1 204 1.23e-24 97.1
Msa0893840 MtrunA17_Chr6g0477751 35.874 223 122 12 1 211 1 214 3.03e-22 90.1
Msa0893840 MtrunA17_Chr6g0452521 37.736 212 112 12 1 201 33 235 6.40e-22 90.1
Msa0893840 MtrunA17_Chr6g0476871 36.735 196 107 10 18 201 18 208 5.47e-21 87.0
Msa0893840 MtrunA17_Chr6g0467781 35.359 181 100 8 39 212 3 173 1.27e-20 84.7
Msa0893840 MtrunA17_Chr6g0476791 36.620 213 102 14 6 198 9 208 1.79e-19 82.8
Msa0893840 MtrunA17_Chr1g0163381 35.417 192 106 12 11 188 11 198 6.63e-15 70.9
Msa0893840 MtrunA17_Chr7g0228581 33.721 172 97 8 29 189 27 192 1.50e-14 69.3
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 56 sgRNAs with CRISPR-Local

Find 60 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TGAGTAAGAAATACTTTATT+TGG 0.169494 6_1:-78705113 Msa0893840:CDS
GGTATTGGTGGTGGTGTTAA+TGG 0.238618 6_1:-78704847 Msa0893840:CDS
CCTGGTTTATGTAATAATAT+TGG 0.276379 6_1:-78704736 Msa0893840:CDS
TCCAAGTGGGTGGTAGTTAA+AGG 0.301512 6_1:-78704892 Msa0893840:CDS
GGTAAGTAATGTAGGGTTCA+TGG 0.354211 6_1:+78705236 None:intergenic
TATTCAAACTACAGATCTTC+CGG 0.354335 6_1:+78704615 None:intergenic
ACAACTTGAGTAAAGGATAA+TGG 0.359989 6_1:+78705174 None:intergenic
TATTTCTTACTCACAAGAAC+GGG 0.363139 6_1:+78705123 None:intergenic
ATTGAACCATGGGTAGGTAT+TGG 0.417221 6_1:-78704862 Msa0893840:CDS
TAGAGGGTGGTAAGTAATGT+AGG 0.427202 6_1:+78705228 None:intergenic
AATGGTAAGAGTATTATAGA+TGG 0.435603 6_1:-78704829 Msa0893840:CDS
ACCTTTAACTACCACCCACT+TGG 0.461157 6_1:+78704891 None:intergenic
TCAATGAATACAACTTCAAA+GGG 0.470712 6_1:+78704658 None:intergenic
ATCAATGAATACAACTTCAA+AGG 0.473477 6_1:+78704657 None:intergenic
GGGCAAAGAGGAAGAAATAG+AGG 0.480997 6_1:+78705211 None:intergenic
TTGGGATAAATGTTAGTGGC+AGG 0.501980 6_1:+78704998 None:intergenic
ACCAGGTGTATCACTGGTGG+TGG 0.503174 6_1:+78704753 None:intergenic
TCTGTTGGGATAAATGTTAG+TGG 0.504722 6_1:+78704994 None:intergenic
TAATGGAAAGTAGGTGGCTA+GGG 0.507074 6_1:+78705191 None:intergenic
TTTAACTACCACCCACTTGG+AGG 0.510750 6_1:+78704894 None:intergenic
AGTAAAGGATAATGGAAAGT+AGG 0.512041 6_1:+78705182 None:intergenic
CAGTCCACCACCACTTTCAC+CGG 0.513171 6_1:+78705086 None:intergenic
GAACCATGGGTAGGTATTGG+TGG 0.518436 6_1:-78704859 Msa0893840:CDS
AGGTGGTTTCATTGAACCAT+GGG 0.524203 6_1:-78704872 Msa0893840:CDS
GTTGAAGATGTTGCTCGATC+CGG 0.529471 6_1:-78704634 Msa0893840:CDS
TTGTTCAACAACTTGAGTAA+AGG 0.539696 6_1:+78705167 None:intergenic
CCACCACCACTTTCACCGGC+TGG 0.539880 6_1:+78705090 None:intergenic
AAATACTTTATTTGGCCAGC+CGG 0.543561 6_1:-78705105 Msa0893840:CDS
ATTTGGCCAGCCGGTGAAAG+TGG 0.544335 6_1:-78705096 Msa0893840:CDS
CCAGCCGGTGAAAGTGGTGG+TGG 0.546062 6_1:-78705090 Msa0893840:CDS
ACATAAACCAGGTGTATCAC+TGG 0.553319 6_1:+78704747 None:intergenic
AAAGCTTGCTGTACAACAAG+TGG 0.555218 6_1:+78705039 None:intergenic
ATAATGGAAAGTAGGTGGCT+AGG 0.557559 6_1:+78705190 None:intergenic
CCATGGGTAGGTATTGGTGG+TGG 0.565594 6_1:-78704856 Msa0893840:CDS
TCAAGTTGTTGAACAAGTGA+AGG 0.568787 6_1:-78705160 Msa0893840:CDS
AAGGTGGTTTCATTGAACCA+TGG 0.574110 6_1:-78704873 Msa0893840:CDS
GTATTTCTTACTCACAAGAA+CGG 0.581176 6_1:+78705122 None:intergenic
TTGTTTAAGATTGAGAGAAG+TGG 0.588206 6_1:-78704805 Msa0893840:CDS
AGAGGGTGGTAAGTAATGTA+GGG 0.588469 6_1:+78705229 None:intergenic
CCAATATTATTACATAAACC+AGG 0.588965 6_1:+78704736 None:intergenic
CCCACCACCAGTGATACACC+TGG 0.602282 6_1:-78704754 Msa0893840:CDS
GTGAAAGTGGTGGTGGACTG+AGG 0.603007 6_1:-78705083 Msa0893840:CDS
AGTAGGTGGCTAGGGCAAAG+AGG 0.612636 6_1:+78705199 None:intergenic
GGTTTCATTGAACCATGGGT+AGG 0.618743 6_1:-78704868 Msa0893840:CDS
AAGTGGGTGGTAGTTAAAGG+TGG 0.629514 6_1:-78704889 Msa0893840:CDS
AAAGGATAATGGAAAGTAGG+TGG 0.636765 6_1:+78705185 None:intergenic
GGCAAAGAGGAAGAAATAGA+GGG 0.646580 6_1:+78705212 None:intergenic
AAAGAGGAAGAAATAGAGGG+TGG 0.652446 6_1:+78705215 None:intergenic
CCACCACCAATACCTACCCA+TGG 0.653181 6_1:+78704856 None:intergenic
TGGCCAGCCGGTGAAAGTGG+TGG 0.668540 6_1:-78705093 Msa0893840:CDS
ATTTCTTACTCACAAGAACG+GGG 0.680212 6_1:+78705124 None:intergenic
TGCTGAATCCTCCAAGTGGG+TGG 0.681258 6_1:-78704902 Msa0893840:CDS
CCAGGTGTATCACTGGTGGT+GGG 0.686983 6_1:+78704754 None:intergenic
TAAACCAGGTGTATCACTGG+TGG 0.706773 6_1:+78704750 None:intergenic
ATGTGCTGAATCCTCCAAGT+GGG 0.714019 6_1:-78704905 Msa0893840:CDS
AATGTGCTGAATCCTCCAAG+TGG 0.759346 6_1:-78704906 Msa0893840:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! AGATTTTTAGATAATGAAAA+TGG - chr6_1:78705140-78705159 Msa0893840:CDS 15.0%
!! TGAGTAAGAAATACTTTATT+TGG - chr6_1:78704739-78704758 Msa0893840:CDS 20.0%
!!! AATCATTGATATTTTCTGTT+GGG + chr6_1:78704875-78704894 None:intergenic 20.0%
!!! AAATCATTGATATTTTCTGT+TGG + chr6_1:78704876-78704895 None:intergenic 20.0%
!!! AATGGTAAGAGTATTATAGA+TGG - chr6_1:78705023-78705042 Msa0893840:CDS 25.0%
! CCAATATTATTACATAAACC+AGG + chr6_1:78705119-78705138 None:intergenic 25.0%
! CCTGGTTTATGTAATAATAT+TGG - chr6_1:78705116-78705135 Msa0893840:CDS 25.0%
! TCAATGAATACAACTTCAAA+GGG + chr6_1:78705197-78705216 None:intergenic 25.0%
! ATCAATGAATACAACTTCAA+AGG + chr6_1:78705198-78705217 None:intergenic 25.0%
!! AGTAAAGGATAATGGAAAGT+AGG + chr6_1:78704673-78704692 None:intergenic 30.0%
ACAACTTGAGTAAAGGATAA+TGG + chr6_1:78704681-78704700 None:intergenic 30.0%
TTGTTCAACAACTTGAGTAA+AGG + chr6_1:78704688-78704707 None:intergenic 30.0%
GAACAAGTGAAGGATAAAAA+TGG - chr6_1:78704702-78704721 Msa0893840:CDS 30.0%
TATTTCTTACTCACAAGAAC+GGG + chr6_1:78704732-78704751 None:intergenic 30.0%
GTATTTCTTACTCACAAGAA+CGG + chr6_1:78704733-78704752 None:intergenic 30.0%
! TTGTTTAAGATTGAGAGAAG+TGG - chr6_1:78705047-78705066 Msa0893840:CDS 30.0%
!!! ATTGAGAGAAGTGGTTTTTT+TGG - chr6_1:78705056-78705075 Msa0893840:CDS 30.0%
!! AAAGGATAATGGAAAGTAGG+TGG + chr6_1:78704670-78704689 None:intergenic 35.0%
! TCAAGTTGTTGAACAAGTGA+AGG - chr6_1:78704692-78704711 Msa0893840:CDS 35.0%
ATTTCTTACTCACAAGAACG+GGG + chr6_1:78704731-78704750 None:intergenic 35.0%
! AAATACTTTATTTGGCCAGC+CGG - chr6_1:78704747-78704766 Msa0893840:CDS 35.0%
!! TGTACAGCAAGCTTTTTCTA+AGG - chr6_1:78704821-78704840 Msa0893840:CDS 35.0%
TCTGTTGGGATAAATGTTAG+TGG + chr6_1:78704861-78704880 None:intergenic 35.0%
AGAGGGTGGTAAGTAATGTA+GGG + chr6_1:78704626-78704645 None:intergenic 40.0%
TAGAGGGTGGTAAGTAATGT+AGG + chr6_1:78704627-78704646 None:intergenic 40.0%
AAAGAGGAAGAAATAGAGGG+TGG + chr6_1:78704640-78704659 None:intergenic 40.0%
GGCAAAGAGGAAGAAATAGA+GGG + chr6_1:78704643-78704662 None:intergenic 40.0%
TAATGGAAAGTAGGTGGCTA+GGG + chr6_1:78704664-78704683 None:intergenic 40.0%
! ATAATGGAAAGTAGGTGGCT+AGG + chr6_1:78704665-78704684 None:intergenic 40.0%
!! AAAGCTTGCTGTACAACAAG+TGG + chr6_1:78704816-78704835 None:intergenic 40.0%
TTGGGATAAATGTTAGTGGC+AGG + chr6_1:78704857-78704876 None:intergenic 40.0%
AAGGTGGTTTCATTGAACCA+TGG - chr6_1:78704979-78704998 Msa0893840:CDS 40.0%
AGGTGGTTTCATTGAACCAT+GGG - chr6_1:78704980-78704999 Msa0893840:CDS 40.0%
ATTGAACCATGGGTAGGTAT+TGG - chr6_1:78704990-78705009 Msa0893840:CDS 40.0%
ACATAAACCAGGTGTATCAC+TGG + chr6_1:78705108-78705127 None:intergenic 40.0%
GGGCAAAGAGGAAGAAATAG+AGG + chr6_1:78704644-78704663 None:intergenic 45.0%
AATGTGCTGAATCCTCCAAG+TGG - chr6_1:78704946-78704965 Msa0893840:CDS 45.0%
ATGTGCTGAATCCTCCAAGT+GGG - chr6_1:78704947-78704966 Msa0893840:CDS 45.0%
TTTAACTACCACCCACTTGG+AGG + chr6_1:78704961-78704980 None:intergenic 45.0%
TCCAAGTGGGTGGTAGTTAA+AGG - chr6_1:78704960-78704979 Msa0893840:CDS 45.0%
ACCTTTAACTACCACCCACT+TGG + chr6_1:78704964-78704983 None:intergenic 45.0%
AAGTGGGTGGTAGTTAAAGG+TGG - chr6_1:78704963-78704982 Msa0893840:CDS 45.0%
GGTTTCATTGAACCATGGGT+AGG - chr6_1:78704984-78705003 Msa0893840:CDS 45.0%
!! GGTATTGGTGGTGGTGTTAA+TGG - chr6_1:78705005-78705024 Msa0893840:CDS 45.0%
TAAACCAGGTGTATCACTGG+TGG + chr6_1:78705105-78705124 None:intergenic 45.0%
GTTGAAGATGTTGCTCGATC+CGG - chr6_1:78705218-78705237 Msa0893840:CDS 45.0%
!! GAACCATGGGTAGGTATTGG+TGG - chr6_1:78704993-78705012 Msa0893840:CDS 50.0%
AGTAGGTGGCTAGGGCAAAG+AGG + chr6_1:78704656-78704675 None:intergenic 55.0%
ATTTGGCCAGCCGGTGAAAG+TGG - chr6_1:78704756-78704775 Msa0893840:CDS 55.0%
CAGTCCACCACCACTTTCAC+CGG + chr6_1:78704769-78704788 None:intergenic 55.0%
!! GTGAAAGTGGTGGTGGACTG+AGG - chr6_1:78704769-78704788 Msa0893840:CDS 55.0%
TGCTGAATCCTCCAAGTGGG+TGG - chr6_1:78704950-78704969 Msa0893840:CDS 55.0%
CCACCACCAATACCTACCCA+TGG + chr6_1:78704999-78705018 None:intergenic 55.0%
!! CCATGGGTAGGTATTGGTGG+TGG - chr6_1:78704996-78705015 Msa0893840:CDS 55.0%
CCAGGTGTATCACTGGTGGT+GGG + chr6_1:78705101-78705120 None:intergenic 55.0%
ACCAGGTGTATCACTGGTGG+TGG + chr6_1:78705102-78705121 None:intergenic 55.0%
CCCACCACCAGTGATACACC+TGG - chr6_1:78705098-78705117 Msa0893840:CDS 60.0%
TGGCCAGCCGGTGAAAGTGG+TGG - chr6_1:78704759-78704778 Msa0893840:CDS 65.0%
CCACCACCACTTTCACCGGC+TGG + chr6_1:78704765-78704784 None:intergenic 65.0%
CCAGCCGGTGAAAGTGGTGG+TGG - chr6_1:78704762-78704781 Msa0893840:CDS 65.0%
Chromosome Type Strat End Strand Name
chr6_1 gene 78704618 78705256 78704618 ID=Msa0893840;Name=Msa0893840
chr6_1 mRNA 78704618 78705256 78704618 ID=Msa0893840-mRNA-1;Parent=Msa0893840;Name=Msa0893840-mRNA-1;_AED=0.33;_eAED=0.33;_QI=0|-1|0|1|-1|1|1|0|212
chr6_1 exon 78704618 78705256 78704618 ID=Msa0893840-mRNA-1:exon:13152;Parent=Msa0893840-mRNA-1
chr6_1 CDS 78704618 78705256 78704618 ID=Msa0893840-mRNA-1:cds;Parent=Msa0893840-mRNA-1
Gene Sequence

>Msa0893840

ATGAACCCTACATTACTTACCACCCTCTATTTCTTCCTCTTTGCCCTAGCCACCTACTTTCCATTATCCTTTACTCAAGTTGTTGAACAAGTGAAGGATAAAAATGGAAACCCCGTTCTTGTGAGTAAGAAATACTTTATTTGGCCAGCCGGTGAAAGTGGTGGTGGACTGAGGCTTAATGAGACAGAAGAATGTCCACTTGTTGTACAGCAAGCTTTTTCTAAGGATGTTAAAAGCCTGCCACTAACATTTATCCCAACAGAAAATATCAATGATTTCATCTTTACTCGCTTCACATCACTAGATATTGTATTTGAAAAGAAGACAAAATGTGCTGAATCCTCCAAGTGGGTGGTAGTTAAAGGTGGTTTCATTGAACCATGGGTAGGTATTGGTGGTGGTGTTAATGGTAAGAGTATTATAGATGGTTTGTTTAAGATTGAGAGAAGTGGTTTTTTTGGATACAAGCTTGTGTTTTGTCCCACCACCAGTGATACACCTGGTTTATGTAATAATATTGGAAGATTTTTAGATAATGAAAATGGAGTGCGTTTGATCATGAGTGAAAATTTTCAACCCTTTGAAGTTGTATTCATTGATGTTGAAGATGTTGCTCGATCCGGAAGATCTGTAGTTTGA

Protein sequence

>Msa0893840

MNPTLLTTLYFFLFALATYFPLSFTQVVEQVKDKNGNPVLVSKKYFIWPAGESGGGLRLNETEECPLVVQQAFSKDVKSLPLTFIPTENINDFIFTRFTSLDIVFEKKTKCAESSKWVVVKGGFIEPWVGIGGGVNGKSIIDGLFKIERSGFFGYKLVFCPTTSDTPGLCNNIGRFLDNENGVRLIMSENFQPFEVVFIDVEDVARSGRSVV*