AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene004245

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene004245.t1 MTR_2g016020 97.619 168 4 0 1 168 1 168 2.55e-120 336
MS.gene004245.t1 MTR_2g077940 35.928 167 88 4 8 161 11 171 2.81e-27 100
MS.gene004245.t1 MTR_2g077960 36.025 161 90 4 8 161 11 165 4.50e-27 100
MS.gene004245.t1 MTR_3g087540 34.091 132 79 5 28 155 25 152 6.91e-22 86.7
MS.gene004245.t1 MTR_3g073990 32.911 158 102 2 1 157 1 155 1.28e-21 86.3
MS.gene004245.t1 MTR_0390s0010 35.032 157 92 2 8 161 11 160 2.86e-19 80.1
MS.gene004245.t1 MTR_0786s0020 34.395 157 93 2 8 161 11 160 2.01e-18 77.8
MS.gene004245.t1 MTR_2g450190 33.758 157 91 3 8 161 11 157 3.47e-16 72.0
MS.gene004245.t1 MTR_0390s0040 33.758 157 91 3 8 161 11 157 3.47e-16 72.0
MS.gene004245.t1 MTR_2g077080 31.915 141 87 2 23 161 31 164 4.76e-14 66.2
MS.gene004245.t1 MTR_1678s0010 28.082 146 95 5 28 168 38 178 1.37e-11 60.1
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene004245.t1 AT1G29140 49.412 170 80 4 1 164 1 170 2.26e-50 159
MS.gene004245.t1 AT5G45880 53.571 140 63 2 27 164 34 173 8.99e-50 158
MS.gene004245.t1 AT4G18596 47.953 171 82 4 1 164 1 171 1.16e-49 158
MS.gene004245.t1 AT4G18596 47.953 171 82 4 1 164 47 217 6.37e-49 157
MS.gene004245.t1 AT4G08685 39.241 158 89 5 8 162 6 159 1.88e-31 111
MS.gene004245.t1 AT5G10130 37.349 166 94 3 1 162 1 160 6.64e-28 102
MS.gene004245.t1 AT1G78040 32.143 168 103 5 1 162 1 163 4.30e-21 85.1
MS.gene004245.t1 AT1G78040 32.143 168 103 5 1 162 1 163 4.30e-21 85.1
MS.gene004245.t1 AT1G78040 32.143 168 103 5 1 162 1 163 4.30e-21 85.1

Find 41 sgRNAs with CRISPR-Local

Find 57 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTGAGAACCTCACCACATTT+AGG 0.300765 2.4:+68962937 None:intergenic
CGGTCAATCTGGTGATGAAT+TGG 0.316647 2.4:+68963619 None:intergenic
GTGGAATGCAAAGAAGAAAA+TGG 0.335509 2.4:-68963207 MS.gene004245:CDS
AGAGGGCTAGCAGCACGAAC+TGG 0.354642 2.4:+68962985 None:intergenic
CCTGAACGCTTCTTTGTAGA+AGG 0.366196 2.4:-68963669 MS.gene004245:CDS
AAATACAGTGTGGAGATAGA+TGG 0.398924 2.4:-68963141 MS.gene004245:CDS
GTTCGTGCTGCTAGCCCTCT+TGG 0.402448 2.4:-68962982 MS.gene004245:CDS
TAGGTAGACGCTCTTTCTTA+AGG 0.405456 2.4:+68962956 None:intergenic
TGATCCTAGCAGCTTGTTGT+AGG 0.405713 2.4:+68963037 None:intergenic
TTCAATGAACTCGGTCAATC+TGG 0.407937 2.4:+68963608 None:intergenic
TACAAAGAAGCGTTCAGGCT+TGG 0.439377 2.4:+68963674 None:intergenic
GAACTTGGAATTAATGAAGA+TGG 0.440677 2.4:-68962913 MS.gene004245:CDS
ACCTCTGAGCAATCTTTCCT+TGG 0.443518 2.4:+68963075 None:intergenic
GAAGCAACAACAGATAAATC+AGG 0.454577 2.4:-68963165 MS.gene004245:CDS
TAATGAAGATGGAACTGAAA+AGG 0.471543 2.4:-68962902 MS.gene004245:CDS
CCTTCTACAAAGAAGCGTTC+AGG 0.474728 2.4:+68963669 None:intergenic
GGAATAAGCCGCACCTAAGA+AGG 0.479861 2.4:+68963695 None:intergenic
GAGGGCTAGCAGCACGAACT+GGG 0.491624 2.4:+68962986 None:intergenic
AGATTGACCGAGTTCATTGA+AGG 0.500832 2.4:-68963606 MS.gene004245:intron
GGTGAGGTTCTCAAAGAACT+TGG 0.517638 2.4:-68962928 MS.gene004245:CDS
GGTCAATCTGGTGATGAATT+GGG 0.518245 2.4:+68963620 None:intergenic
CTTCACATGTTTCATCCTCA+TGG 0.533134 2.4:+68963115 None:intergenic
TTATTCTTTGCAAGAGTCCA+AGG 0.534437 2.4:-68963092 MS.gene004245:CDS
AAAAGCAAAGGGTGAAGACA+AGG 0.570670 2.4:+68963721 None:intergenic
TGAAGGTGCAACGGTGCGTG+TGG 0.602260 2.4:-68963226 MS.gene004245:intron
CTTTCTTAAGGAAACCAAGA+GGG 0.608256 2.4:+68962968 None:intergenic
ATCAGTGTCACAAACAACAA+TGG 0.613848 2.4:-68963018 MS.gene004245:CDS
AAGCAAAGGGTGAAGACAAG+GGG 0.617019 2.4:+68963723 None:intergenic
CTCACCTACAACAAGCTGCT+AGG 0.622703 2.4:-68963041 MS.gene004245:CDS
TGAAGATGGAACTGAAAAGG+AGG 0.627791 2.4:-68962899 MS.gene004245:CDS
GTACGTACCTTCAATGAACT+CGG 0.638216 2.4:+68963599 None:intergenic
AAAGAGCGTCTACCTAAATG+TGG 0.642536 2.4:-68962949 MS.gene004245:CDS
AGGGCTAGCAGCACGAACTG+GGG 0.655258 2.4:+68962987 None:intergenic
TATATGTAATGAAGGTGCAA+CGG 0.656510 2.4:-68963235 MS.gene004245:intron
AAAGCAAAGGGTGAAGACAA+GGG 0.660463 2.4:+68963722 None:intergenic
GCGTCTACCTAAATGTGGTG+AGG 0.675591 2.4:-68962944 MS.gene004245:CDS
TCTTTCTTAAGGAAACCAAG+AGG 0.685975 2.4:+68962967 None:intergenic
TAAATCAGGAAAATACAGTG+TGG 0.693438 2.4:-68963151 MS.gene004245:CDS
TCCAAGGAAAGATTGCTCAG+AGG 0.698789 2.4:-68963076 MS.gene004245:CDS
AGCAAAGGGTGAAGACAAGG+GGG 0.721824 2.4:+68963724 None:intergenic
GGAGATAGATGGAGACCATG+AGG 0.745188 2.4:-68963130 MS.gene004245:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! ATAATCTGAATTTTACTTTT+AGG + chr2.4:68963240-68963259 None:intergenic 15.0%
!!! GACATAAATAATAATTTTTG+TGG - chr2.4:68963374-68963393 MS.gene004245:intron 15.0%
! ACACATTTATTACTAAGAAG+CGG - chr2.4:68963300-68963319 MS.gene004245:intron 25.0%
! TAAGAAGGATAAAAAGCAAA+GGG + chr2.4:68962928-68962947 None:intergenic 25.0%
!!! TTTTACTTTTAGGTATTACG+AGG + chr2.4:68963230-68963249 None:intergenic 25.0%
CTAAGAAGGATAAAAAGCAA+AGG + chr2.4:68962929-68962948 None:intergenic 30.0%
GAACTTGGAATTAATGAAGA+TGG - chr2.4:68963722-68963741 MS.gene004245:CDS 30.0%
TAAATCAGGAAAATACAGTG+TGG - chr2.4:68963484-68963503 MS.gene004245:intron 30.0%
TAATGAAGATGGAACTGAAA+AGG - chr2.4:68963733-68963752 MS.gene004245:CDS 30.0%
TTGCACCTTCATTACATATA+TGG + chr2.4:68963400-68963419 None:intergenic 30.0%
! TATATGTAATGAAGGTGCAA+CGG - chr2.4:68963400-68963419 MS.gene004245:intron 30.0%
!!! CTTTGCTTTTTATCCTTCTT+AGG - chr2.4:68962927-68962946 MS.gene004245:CDS 30.0%
AAATACAGTGTGGAGATAGA+TGG - chr2.4:68963494-68963513 MS.gene004245:intron 35.0%
ACACGATACATATTTGACAC+CGG + chr2.4:68963116-68963135 None:intergenic 35.0%
ATATATGTGACAGTGTGTGT+TGG + chr2.4:68963145-68963164 None:intergenic 35.0%
ATCAGTGTCACAAACAACAA+TGG - chr2.4:68963617-68963636 MS.gene004245:CDS 35.0%
CTTTCTTAAGGAAACCAAGA+GGG + chr2.4:68963670-68963689 None:intergenic 35.0%
GAAGCAACAACAGATAAATC+AGG - chr2.4:68963470-68963489 MS.gene004245:intron 35.0%
GTGGAATGCAAAGAAGAAAA+TGG - chr2.4:68963428-68963447 MS.gene004245:intron 35.0%
TCTTTCTTAAGGAAACCAAG+AGG + chr2.4:68963671-68963690 None:intergenic 35.0%
TGTGGCCATATATGTAATGA+AGG - chr2.4:68963392-68963411 MS.gene004245:intron 35.0%
TTATTCTTTGCAAGAGTCCA+AGG - chr2.4:68963543-68963562 MS.gene004245:intron 35.0%
! CTTTTTATCCTTCTTAGGTG+CGG - chr2.4:68962932-68962951 MS.gene004245:CDS 35.0%
AAAAGCAAAGGGTGAAGACA+AGG + chr2.4:68962917-68962936 None:intergenic 40.0%
AAAGCAAAGGGTGAAGACAA+GGG + chr2.4:68962916-68962935 None:intergenic 40.0%
AGATTGACCGAGTTCATTGA+AGG - chr2.4:68963029-68963048 MS.gene004245:CDS 40.0%
CTTCACATGTTTCATCCTCA+TGG + chr2.4:68963523-68963542 None:intergenic 40.0%
GCAAGACATTCGATATGCTA+AGG + chr2.4:68963349-68963368 None:intergenic 40.0%
GTACGTACCTTCAATGAACT+CGG + chr2.4:68963039-68963058 None:intergenic 40.0%
TAGGTAGACGCTCTTTCTTA+AGG + chr2.4:68963682-68963701 None:intergenic 40.0%
TATACTCCTCGAATTATGCG+TGG - chr2.4:68963089-68963108 MS.gene004245:CDS 40.0%
TGAAGATGGAACTGAAAAGG+AGG - chr2.4:68963736-68963755 MS.gene004245:CDS 40.0%
TTCAATGAACTCGGTCAATC+TGG + chr2.4:68963030-68963049 None:intergenic 40.0%
TTGAGAACCTCACCACATTT+AGG + chr2.4:68963701-68963720 None:intergenic 40.0%
! GGTCAATCTGGTGATGAATT+GGG + chr2.4:68963018-68963037 None:intergenic 40.0%
!! AAAGAGCGTCTACCTAAATG+TGG - chr2.4:68963686-68963705 MS.gene004245:CDS 40.0%
AAGCAAAGGGTGAAGACAAG+GGG + chr2.4:68962915-68962934 None:intergenic 45.0%
ACCTCTGAGCAATCTTTCCT+TGG + chr2.4:68963563-68963582 None:intergenic 45.0%
CCTGAACGCTTCTTTGTAGA+AGG - chr2.4:68962966-68962985 MS.gene004245:CDS 45.0%
GGTGAGGTTCTCAAAGAACT+TGG - chr2.4:68963707-68963726 MS.gene004245:CDS 45.0%
TCCAAGGAAAGATTGCTCAG+AGG - chr2.4:68963559-68963578 MS.gene004245:intron 45.0%
! CGGTCAATCTGGTGATGAAT+TGG + chr2.4:68963019-68963038 None:intergenic 45.0%
!! CCTTCTACAAAGAAGCGTTC+AGG + chr2.4:68962969-68962988 None:intergenic 45.0%
!! TACAAAGAAGCGTTCAGGCT+TGG + chr2.4:68962964-68962983 None:intergenic 45.0%
!! TGATCCTAGCAGCTTGTTGT+AGG + chr2.4:68963601-68963620 None:intergenic 45.0%
AGCAAAGGGTGAAGACAAGG+GGG + chr2.4:68962914-68962933 None:intergenic 50.0%
CTCACCTACAACAAGCTGCT+AGG - chr2.4:68963594-68963613 MS.gene004245:intron 50.0%
GCGTCTACCTAAATGTGGTG+AGG - chr2.4:68963691-68963710 MS.gene004245:CDS 50.0%
GGAATAAGCCGCACCTAAGA+AGG + chr2.4:68962943-68962962 None:intergenic 50.0%
GGAGATAGATGGAGACCATG+AGG - chr2.4:68963505-68963524 MS.gene004245:intron 50.0%
TCCTCGAATTATGCGTGGTC+CGG - chr2.4:68963094-68963113 MS.gene004245:CDS 50.0%
ACCGGACCACGCATAATTCG+AGG + chr2.4:68963098-68963117 None:intergenic 55.0%
! AGAGGGCTAGCAGCACGAAC+TGG + chr2.4:68963653-68963672 None:intergenic 60.0%
! AGGGCTAGCAGCACGAACTG+GGG + chr2.4:68963651-68963670 None:intergenic 60.0%
! GAGGGCTAGCAGCACGAACT+GGG + chr2.4:68963652-68963671 None:intergenic 60.0%
! GTTCGTGCTGCTAGCCCTCT+TGG - chr2.4:68963653-68963672 MS.gene004245:CDS 60.0%
! TGAAGGTGCAACGGTGCGTG+TGG - chr2.4:68963409-68963428 MS.gene004245:intron 60.0%


Chromosome Type Strat End Strand Name
chr2.4 gene 68962894 68963763 68962894 ID=MS.gene004245
chr2.4 mRNA 68962894 68963763 68962894 ID=MS.gene004245.t1;Parent=MS.gene004245
chr2.4 exon 68963607 68963763 68963607 ID=MS.gene004245.t1.exon1;Parent=MS.gene004245.t1
chr2.4 CDS 68963607 68963763 68963607 ID=cds.MS.gene004245.t1;Parent=MS.gene004245.t1
chr2.4 exon 68962894 68963243 68962894 ID=MS.gene004245.t1.exon2;Parent=MS.gene004245.t1
chr2.4 CDS 68962894 68963243 68962894 ID=cds.MS.gene004245.t1;Parent=MS.gene004245.t1
Gene Sequence

>MS.gene004245

ATGGCAAAGTCTACAATCCCCCTTGTCTTCACCCTTTGCTTTTTATCCTTCTTAGGTGCGGCTTATTCCAAGCCTGAACGCTTCTTTGTAGAAGGTGTTGTTTACTGTGACACATGTCGCACCCAATTCATCACCAGATTGACCGAGTTCATTGAAGGTACGTACATATTTTTTAATGTGAATCTATGAAGCACATATACTCCTCGAATTATGCGTGGTCCGGTGTCAAATATGTATCGTGTCTGACACCAACACACACTGTCACATATATGTCATTTTCTTAAATTATTATCGATGTTCACATGTCATGTCGTGTCTAGTGTATAGTCTGTGCCTCGTAATACCTAAAAGTAAAATTCAGATTATTGATTTTTATTTTTTTAAAGAGTCTAACGATGAAACTCACACACATTTATTACTAAGAAGCGGAGAATTAAGAGTTCTAACTCGTGCCTTAGCATATCGAATGTCTTGCAACTTGACATAAATAATAATTTTTGTGGCCATATATGTAATGAAGGTGCAACGGTGCGTGTGGAATGCAAAGAAGAAAATGGAACATTGACATTCAACAAAGAAGCAACAACAGATAAATCAGGAAAATACAGTGTGGAGATAGATGGAGACCATGAGGATGAAACATGTGAAGTTATTCTTTGCAAGAGTCCAAGGAAAGATTGCTCAGAGGTTGACTCAGAAGCTCACCTACAACAAGCTGCTAGGATCAGTGTCACAAACAACAATGGAATTGTGTCCCCAGTTCGTGCTGCTAGCCCTCTTGGTTTCCTTAAGAAAGAGCGTCTACCTAAATGTGGTGAGGTTCTCAAAGAACTTGGAATTAATGAAGATGGAACTGAAAAGGAGGACTAG
Protein sequence

>MS.gene004245.t1

MAKSTIPLVFTLCFLSFLGAAYSKPERFFVEGVVYCDTCRTQFITRLTEFIEGATVRVECKEENGTLTFNKEATTDKSGKYSVEIDGDHEDETCEVILCKSPRKDCSEVDSEAHLQQAARISVTNNNGIVSPVRAASPLGFLKKERLPKCGEVLKELGINEDGTEKED