AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1192100

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1192100 MtrunA17_Chr8g0362131 98.913 92 1 0 1 92 1 92 1.47e-61 182
Msa1192100 MtrunA17_Chr5g0416431 82.051 78 13 1 16 92 16 93 1.76e-39 126
Msa1192100 MtrunA17_Chr7g0217141 75.532 94 21 2 1 93 1 93 2.08e-38 123
Msa1192100 MtrunA17_Chr6g0453041 74.359 78 19 1 17 93 15 92 3.15e-32 107
Msa1192100 MtrunA17_Chr3g0093001 71.795 78 19 2 17 93 17 92 4.77e-31 104
Msa1192100 MtrunA17_Chr7g0237771 50.617 81 34 3 1 80 1 76 4.47e-13 59.3
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1192100 AT3G47710.1 69.474 95 24 3 1 93 1 92 6.55e-37 120
Msa1192100 AT3G28857.1 65.957 94 28 2 1 92 1 92 8.25e-36 117
Msa1192100 AT1G26945.1 78.378 74 15 1 19 91 19 92 1.31e-33 111
Msa1192100 AT5G15160.1 68.000 75 22 1 19 91 18 92 1.54e-31 106
Msa1192100 AT1G74500.1 73.418 79 17 2 17 93 17 93 1.94e-31 106
Msa1192100 AT5G39860.1 66.667 78 24 1 17 92 15 92 8.37e-31 104

Find 63 sgRNAs with CRISPR-Local

Find 106 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ATTATCATCAACCTCTCTTA+TGG 0.222402 8_1:+37351565 Msa1192100:three_prime_UTR
CTATGTCCCTATGGGGTTAA+AGG 0.239605 8_1:-37349707 None:intergenic
TGACCGATTGTCACAACTTT+TGG 0.247784 8_1:+37351400 Msa1192100:CDS
GGCTAGGCAAGTTATTAAAT+AGG 0.271481 8_1:-37349798 None:intergenic
TAGTGTTAATTAGTGTGATA+TGG 0.314949 8_1:+37351654 Msa1192100:three_prime_UTR
TTGAGCACTGTTAGGGTCTA+TGG 0.329793 8_1:-37351426 None:intergenic
AGCTAGTGAGACATATTAAA+AGG 0.335554 8_1:-37351525 None:intergenic
CCATAGGGACATAGGCAAAA+AGG 0.345676 8_1:+37349716 Msa1192100:five_prime_UTR
AAAGTGTTTGAGAAAGGTAT+TGG 0.351552 8_1:-37349820 None:intergenic
ATAGCTGCTTGAGCACTGTT+AGG 0.352323 8_1:-37351434 None:intergenic
GGGAGACAAGTAAATGAAAT+AGG 0.357899 8_1:-37349763 None:intergenic
TTACAAAATGTCTAAAGAAC+GGG 0.367735 8_1:-37351717 None:intergenic
AACTTGTACCTGAACTTTCA+AGG 0.399081 8_1:+37350301 Msa1192100:CDS
GCTAGGCAAGTTATTAAATA+GGG 0.401242 8_1:-37349797 None:intergenic
TGGGAACGCCTTGAAAGTTC+AGG 0.406573 8_1:-37350309 None:intergenic
ACAACCTAATCTCTCTTTCA+TGG 0.408857 8_1:+37349884 Msa1192100:five_prime_UTR
TTATCATCAACCTCTCTTAT+GGG 0.416206 8_1:+37351566 Msa1192100:three_prime_UTR
AGAAAATTATTATACCTTAT+GGG 0.418461 8_1:-37350328 None:intergenic
GATGGACGAGAGAGAGAAAA+GGG 0.419581 8_1:-37349910 None:intergenic
GTGCTCAAGCAGCTATCATT+AGG 0.423047 8_1:+37351441 Msa1192100:CDS
AAAGAGGTCCCCATGCAGTT+GGG 0.423561 8_1:+37349655 Msa1192100:five_prime_UTR
CATGGGGACCTCTTTGTGTC+AGG 0.427728 8_1:-37349647 None:intergenic
CTTTAACCCCATAGGGACAT+AGG 0.429504 8_1:+37349708 Msa1192100:five_prime_UTR
TCTTCTGCTAGACATTGTTA+AGG 0.430216 8_1:-37350202 None:intergenic
AAGTGTTTGAGAAAGGTATT+GGG 0.430347 8_1:-37349819 None:intergenic
ACTTTCAAGGCGTTCCCATA+AGG 0.475795 8_1:+37350314 Msa1192100:CDS
ATTGTAGGTTTCAGCTGCTA+AGG 0.479345 8_1:+37351319 Msa1192100:intron
TTAATTCAATAGTGAGATTG+AGG 0.480176 8_1:+37351625 Msa1192100:three_prime_UTR
AGATCTCGTTCAAGACAATC+TGG 0.480776 8_1:+37350222 Msa1192100:CDS
AGGATAAAAGTGTTTGAGAA+AGG 0.482084 8_1:-37349826 None:intergenic
AGGTACAAGTTGTTGTAACT+TGG 0.482816 8_1:-37350289 None:intergenic
CAAGTAAATGAAATAGGAAT+GGG 0.484041 8_1:-37349757 None:intergenic
AAGAGGTCCCCATGCAGTTG+GGG 0.496582 8_1:+37349656 Msa1192100:five_prime_UTR
TTTGAGAAAGGTATTGGGCT+AGG 0.496830 8_1:-37349814 None:intergenic
TGATGGACGAGAGAGAGAAA+AGG 0.497265 8_1:-37349911 None:intergenic
TAGAGTCTAGGTAGCTACTT+AGG 0.512562 8_1:-37350036 None:intergenic
ACAAGTAAATGAAATAGGAA+TGG 0.513976 8_1:-37349758 None:intergenic
TTCTCAGCTGAGACAAGTGA+TGG 0.516764 8_1:-37349928 None:intergenic
TAGCTGCTTGAGCACTGTTA+GGG 0.522205 8_1:-37351433 None:intergenic
TTGAAGGAAACCTAGAGTCT+AGG 0.523348 8_1:-37350048 None:intergenic
CAAAGAGGTCCCCATGCAGT+TGG 0.525978 8_1:+37349654 Msa1192100:five_prime_UTR
ACATTTCCTTTAACCCCATA+GGG 0.527841 8_1:+37349701 Msa1192100:five_prime_UTR
GTAGCCATGAAAGAGAGATT+AGG 0.531428 8_1:-37349888 None:intergenic
GAGGTCCCCATGCAGTTGGG+GGG 0.536452 8_1:+37349658 Msa1192100:five_prime_UTR
TAAGTAGCTACCTAGACTCT+AGG 0.537832 8_1:+37350038 Msa1192100:five_prime_UTR
GAGAATGTGTCAGTTGGTGT+TGG 0.544938 8_1:-37349858 None:intergenic
TGTCCAAAAGTTGTGACAAT+CGG 0.545364 8_1:-37351403 None:intergenic
AGAGGTCCCCATGCAGTTGG+GGG 0.547715 8_1:+37349657 Msa1192100:five_prime_UTR
CACATTTCCTTTAACCCCAT+AGG 0.548119 8_1:+37349700 Msa1192100:five_prime_UTR
GTTACAAAATGTCTAAAGAA+CGG 0.552336 8_1:-37351718 None:intergenic
GTTGGTGTTGGAAGTTGAAG+AGG 0.564686 8_1:-37349846 None:intergenic
AGGTCCCCATGCAGTTGGGG+GGG 0.573436 8_1:+37349659 Msa1192100:five_prime_UTR
TGTTAATTAGTGTGATATGG+AGG 0.580992 8_1:+37351657 Msa1192100:three_prime_UTR
TTAAATAGGGATATTACGTG+AGG 0.596488 8_1:-37349784 None:intergenic
TGTTGAGAGAATGTGTCAGT+TGG 0.622998 8_1:-37349864 None:intergenic
GAGACATATTAAAAGGCATG+TGG 0.632495 8_1:-37351518 None:intergenic
TAAATAGGGATATTACGTGA+GGG 0.635260 8_1:-37349783 None:intergenic
CAGTGCATGAGACTTCCACT+AGG 0.648690 8_1:-37351692 None:intergenic
AGGTCACAAACTTCACCTAG+TGG 0.670978 8_1:+37351677 Msa1192100:three_prime_UTR
GAAAACGTTACCCATAAGAG+AGG 0.673444 8_1:-37351576 None:intergenic
TACAAAATGTCTAAAGAACG+GGG 0.685856 8_1:-37351716 None:intergenic
GTGCTGAGCCTGACACAAAG+AGG 0.709169 8_1:+37349639 None:intergenic
TTGAGCATCAGAGATCTCAG+TGG 0.738554 8_1:-37350250 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TAGCTTTTTTTTTTTTTTGA+AGG - chr8_1:37350067-37350086 None:intergenic 15.0%
!! AGAAAATTATTATACCTTAT+GGG - chr8_1:37350331-37350350 None:intergenic 15.0%
!! AAGAAAATTATTATACCTTA+TGG - chr8_1:37350332-37350351 None:intergenic 15.0%
!!! AAATCAATTTTATGTGTTTA+GGG - chr8_1:37350432-37350451 None:intergenic 15.0%
!!! AAATTGATTTCTAAAAGATA+TGG + chr8_1:37350442-37350461 Msa1192100:intron 15.0%
!!! TTTTGAATGAAATAAATTTG+AGG - chr8_1:37350642-37350661 None:intergenic 15.0%
!! TTTATTTCATTCAAAATCAA+TGG + chr8_1:37350646-37350665 Msa1192100:intron 15.0%
!!! AAATGATCTTTAATTTTTTC+TGG + chr8_1:37350763-37350782 Msa1192100:intron 15.0%
!!! TAAAAACATATCTTCAATTT+TGG + chr8_1:37350885-37350904 Msa1192100:intron 15.0%
!! TATAATGTTTATTGTATTGT+AGG + chr8_1:37351304-37351323 Msa1192100:intron 15.0%
!!! GAAATCAATTTTATGTGTTT+AGG - chr8_1:37350433-37350452 None:intergenic 20.0%
! CAAGTAAATGAAATAGGAAT+GGG - chr8_1:37349760-37349779 None:intergenic 25.0%
! ACAAGTAAATGAAATAGGAA+TGG - chr8_1:37349761-37349780 None:intergenic 25.0%
!! TAGACATTGTTAAGGTTTTT+GGG - chr8_1:37350197-37350216 None:intergenic 25.0%
! TAAAAGAGAGAATACAGAAA+AGG - chr8_1:37350356-37350375 None:intergenic 25.0%
! AGTTCTTGAAATTATTACGT+AGG - chr8_1:37350791-37350810 None:intergenic 25.0%
!!! AAATTTGTTGTGTTCAAGAA+AGG + chr8_1:37351010-37351029 Msa1192100:intron 25.0%
!!! AATTTGTTGTGTTCAAGAAA+GGG + chr8_1:37351011-37351030 Msa1192100:intron 25.0%
! TTAATTCAATAGTGAGATTG+AGG + chr8_1:37351625-37351644 Msa1192100:three_prime_UTR 25.0%
! TAGTGTTAATTAGTGTGATA+TGG + chr8_1:37351654-37351673 Msa1192100:three_prime_UTR 25.0%
! TTACAAAATGTCTAAAGAAC+GGG - chr8_1:37351720-37351739 None:intergenic 25.0%
! GTTACAAAATGTCTAAAGAA+CGG - chr8_1:37351721-37351740 None:intergenic 25.0%
TAAATAGGGATATTACGTGA+GGG - chr8_1:37349786-37349805 None:intergenic 30.0%
TTAAATAGGGATATTACGTG+AGG - chr8_1:37349787-37349806 None:intergenic 30.0%
GCTAGGCAAGTTATTAAATA+GGG - chr8_1:37349800-37349819 None:intergenic 30.0%
!! AAGTGTTTGAGAAAGGTATT+GGG - chr8_1:37349822-37349841 None:intergenic 30.0%
! AAAGTGTTTGAGAAAGGTAT+TGG - chr8_1:37349823-37349842 None:intergenic 30.0%
!! AGGATAAAAGTGTTTGAGAA+AGG - chr8_1:37349829-37349848 None:intergenic 30.0%
! CTAGACATTGTTAAGGTTTT+TGG - chr8_1:37350198-37350217 None:intergenic 30.0%
GTCAACAAAAAACTTTAGCT+TGG - chr8_1:37350963-37350982 None:intergenic 30.0%
! CAACACACATATTTTATGTG+TGG + chr8_1:37351091-37351110 Msa1192100:intron 30.0%
! ACATATTTTATGTGTGGCTT+TGG + chr8_1:37351097-37351116 Msa1192100:intron 30.0%
! CAACAAATTTTCAGTTGCTA+TGG - chr8_1:37351250-37351269 None:intergenic 30.0%
AGCTAGTGAGACATATTAAA+AGG - chr8_1:37351528-37351547 None:intergenic 30.0%
ATTATCATCAACCTCTCTTA+TGG + chr8_1:37351565-37351584 Msa1192100:three_prime_UTR 30.0%
TTATCATCAACCTCTCTTAT+GGG + chr8_1:37351566-37351585 Msa1192100:three_prime_UTR 30.0%
TGTTAATTAGTGTGATATGG+AGG + chr8_1:37351657-37351676 Msa1192100:three_prime_UTR 30.0%
TACAAAATGTCTAAAGAACG+GGG - chr8_1:37351719-37351738 None:intergenic 30.0%
ACATTTCCTTTAACCCCATA+GGG + chr8_1:37349701-37349720 Msa1192100:five_prime_UTR 35.0%
GGGAGACAAGTAAATGAAAT+AGG - chr8_1:37349766-37349785 None:intergenic 35.0%
GGCTAGGCAAGTTATTAAAT+AGG - chr8_1:37349801-37349820 None:intergenic 35.0%
ACAACCTAATCTCTCTTTCA+TGG + chr8_1:37349884-37349903 Msa1192100:five_prime_UTR 35.0%
!! ATTGTTAAGGTTTTTGGGCT+AGG - chr8_1:37350192-37350211 None:intergenic 35.0%
TCTTCTGCTAGACATTGTTA+AGG - chr8_1:37350205-37350224 None:intergenic 35.0%
AGGTACAAGTTGTTGTAACT+TGG - chr8_1:37350292-37350311 None:intergenic 35.0%
AACTTGTACCTGAACTTTCA+AGG + chr8_1:37350301-37350320 Msa1192100:CDS 35.0%
!!! ATTTTATGTGTGGCTTTGGT+TGG + chr8_1:37351101-37351120 Msa1192100:intron 35.0%
GTAAACGAGTTAAGGATTCA+GGG - chr8_1:37351155-37351174 None:intergenic 35.0%
ATGATGTATGCTTTGCAAGT+GGG - chr8_1:37351212-37351231 None:intergenic 35.0%
AATGATGTATGCTTTGCAAG+TGG - chr8_1:37351213-37351232 None:intergenic 35.0%
CATCAAAAACTTGCATAGAG+AGG + chr8_1:37351364-37351383 Msa1192100:CDS 35.0%
TGTCCAAAAGTTGTGACAAT+CGG - chr8_1:37351406-37351425 None:intergenic 35.0%
! GAGACATATTAAAAGGCATG+TGG - chr8_1:37351521-37351540 None:intergenic 35.0%
CACATTTCCTTTAACCCCAT+AGG + chr8_1:37349700-37349719 Msa1192100:five_prime_UTR 40.0%
! TTTTTGCCTATGTCCCTATG+GGG - chr8_1:37349717-37349736 None:intergenic 40.0%
! CTTTTTGCCTATGTCCCTAT+GGG - chr8_1:37349718-37349737 None:intergenic 40.0%
CATAGGCAAAAAGGACAGTA+TGG + chr8_1:37349725-37349744 Msa1192100:five_prime_UTR 40.0%
!! TTTGAGAAAGGTATTGGGCT+AGG - chr8_1:37349817-37349836 None:intergenic 40.0%
TGTTGAGAGAATGTGTCAGT+TGG - chr8_1:37349867-37349886 None:intergenic 40.0%
GTAGCCATGAAAGAGAGATT+AGG - chr8_1:37349891-37349910 None:intergenic 40.0%
TAGAGTCTAGGTAGCTACTT+AGG - chr8_1:37350039-37350058 None:intergenic 40.0%
TAAGTAGCTACCTAGACTCT+AGG + chr8_1:37350038-37350057 Msa1192100:five_prime_UTR 40.0%
TTGAAGGAAACCTAGAGTCT+AGG - chr8_1:37350051-37350070 None:intergenic 40.0%
!! AAGGTTTTTGGGCTAGGTAT+AGG - chr8_1:37350186-37350205 None:intergenic 40.0%
AGATCTCGTTCAAGACAATC+TGG + chr8_1:37350222-37350241 Msa1192100:CDS 40.0%
TAGTGTGTGTTCGTTCTACA+GGG - chr8_1:37350676-37350695 None:intergenic 40.0%
GGTAAACGAGTTAAGGATTC+AGG - chr8_1:37351156-37351175 None:intergenic 40.0%
GTTTGTGGGTAAACGAGTTA+AGG - chr8_1:37351163-37351182 None:intergenic 40.0%
TCGTTTACCCACAAACTTGT+AGG + chr8_1:37351167-37351186 Msa1192100:intron 40.0%
CGTTTACCCACAAACTTGTA+GGG + chr8_1:37351168-37351187 Msa1192100:intron 40.0%
ATTGTAGGTTTCAGCTGCTA+AGG + chr8_1:37351319-37351338 Msa1192100:intron 40.0%
! TGACCGATTGTCACAACTTT+TGG + chr8_1:37351400-37351419 Msa1192100:CDS 40.0%
GAAAACGTTACCCATAAGAG+AGG - chr8_1:37351579-37351598 None:intergenic 40.0%
CTATGTCCCTATGGGGTTAA+AGG - chr8_1:37349710-37349729 None:intergenic 45.0%
CTTTAACCCCATAGGGACAT+AGG + chr8_1:37349708-37349727 Msa1192100:five_prime_UTR 45.0%
! CCTTTTTGCCTATGTCCCTA+TGG - chr8_1:37349719-37349738 None:intergenic 45.0%
CCATAGGGACATAGGCAAAA+AGG + chr8_1:37349716-37349735 Msa1192100:five_prime_UTR 45.0%
!! GTTGGTGTTGGAAGTTGAAG+AGG - chr8_1:37349849-37349868 None:intergenic 45.0%
! GAGAATGTGTCAGTTGGTGT+TGG - chr8_1:37349861-37349880 None:intergenic 45.0%
GATGGACGAGAGAGAGAAAA+GGG - chr8_1:37349913-37349932 None:intergenic 45.0%
! TGATGGACGAGAGAGAGAAA+AGG - chr8_1:37349914-37349933 None:intergenic 45.0%
TTCTCAGCTGAGACAAGTGA+TGG - chr8_1:37349931-37349950 None:intergenic 45.0%
TTGAGCATCAGAGATCTCAG+TGG - chr8_1:37350253-37350272 None:intergenic 45.0%
! ACTTTCAAGGCGTTCCCATA+AGG + chr8_1:37350314-37350333 Msa1192100:CDS 45.0%
GTAGTGTGTGTTCGTTCTAC+AGG - chr8_1:37350677-37350696 None:intergenic 45.0%
ACTTGTAGGGCTGTGGAATT+CGG + chr8_1:37351181-37351200 Msa1192100:intron 45.0%
! TTGAGCACTGTTAGGGTCTA+TGG - chr8_1:37351429-37351448 None:intergenic 45.0%
! TAGCTGCTTGAGCACTGTTA+GGG - chr8_1:37351436-37351455 None:intergenic 45.0%
! ATAGCTGCTTGAGCACTGTT+AGG - chr8_1:37351437-37351456 None:intergenic 45.0%
GTGCTCAAGCAGCTATCATT+AGG + chr8_1:37351441-37351460 Msa1192100:CDS 45.0%
AGGTCACAAACTTCACCTAG+TGG + chr8_1:37351677-37351696 Msa1192100:three_prime_UTR 45.0%
!! TTAAAATTTAATTAATTCTA+AGG - chr8_1:37350744-37350763 None:intergenic 5.0%
AAAGAGGTCCCCATGCAGTT+GGG + chr8_1:37349655-37349674 Msa1192100:five_prime_UTR 50.0%
TGGGAACGCCTTGAAAGTTC+AGG - chr8_1:37350312-37350331 None:intergenic 50.0%
CCACAGCCCTACAAGTTTGT+GGG - chr8_1:37351177-37351196 None:intergenic 50.0%
TCCACAGCCCTACAAGTTTG+TGG - chr8_1:37351178-37351197 None:intergenic 50.0%
CAGTGCATGAGACTTCCACT+AGG - chr8_1:37351695-37351714 None:intergenic 50.0%
CAAAGAGGTCCCCATGCAGT+TGG + chr8_1:37349654-37349673 Msa1192100:five_prime_UTR 55.0%
AAGAGGTCCCCATGCAGTTG+GGG + chr8_1:37349656-37349675 Msa1192100:five_prime_UTR 55.0%
TAACACCCCCCCAACTGCAT+GGG - chr8_1:37349667-37349686 None:intergenic 55.0%
CCCACAAACTTGTAGGGCTG+TGG + chr8_1:37351174-37351193 Msa1192100:intron 55.0%
AGAGGTCCCCATGCAGTTGG+GGG + chr8_1:37349657-37349676 Msa1192100:five_prime_UTR 60.0%
AACACCCCCCCAACTGCATG+GGG - chr8_1:37349666-37349685 None:intergenic 60.0%
GTAACACCCCCCCAACTGCA+TGG - chr8_1:37349668-37349687 None:intergenic 60.0%
GAGGTCCCCATGCAGTTGGG+GGG + chr8_1:37349658-37349677 Msa1192100:five_prime_UTR 65.0%
AGGTCCCCATGCAGTTGGGG+GGG + chr8_1:37349659-37349678 Msa1192100:five_prime_UTR 65.0%
Chromosome Type Strat End Strand Name
chr8_1 gene 37349648 37351756 37349648 ID=Msa1192100;Name=Msa1192100
chr8_1 mRNA 37349648 37351756 37349648 ID=Msa1192100-mRNA-1;Parent=Msa1192100;Name=Msa1192100-mRNA-1;_AED=0.00;_eAED=0.00;_QI=562|1|1|1|1|1|2|275|93
chr8_1 exon 37349648 37350335 37349648 ID=Msa1192100-mRNA-1:exon:12286;Parent=Msa1192100-mRNA-1
chr8_1 exon 37351326 37351756 37351326 ID=Msa1192100-mRNA-1:exon:12287;Parent=Msa1192100-mRNA-1
chr8_1 five_prime_UTR 37349648 37350209 37349648 ID=Msa1192100-mRNA-1:five_prime_utr;Parent=Msa1192100-mRNA-1
chr8_1 CDS 37350210 37350335 37350210 ID=Msa1192100-mRNA-1:cds;Parent=Msa1192100-mRNA-1
chr8_1 CDS 37351326 37351481 37351326 ID=Msa1192100-mRNA-1:cds;Parent=Msa1192100-mRNA-1
chr8_1 three_prime_UTR 37351482 37351756 37351482 ID=Msa1192100-mRNA-1:three_prime_utr;Parent=Msa1192100-mRNA-1
Gene Sequence

>Msa1192100

ATGTCTAGCAGAAGATCTCGTTCAAGACAATCTGGTGTTTCCACTGAGATCTCTGATGCTCAAATTAATGATCTCGTCACCAAGTTACAACAACTTGTACCTGAACTTTCAAGGCGTTCCCATAAGGTTTCAGCTGCTAAGGTATTGCAAGAGACTTGCAATTACATCAAAAACTTGCATAGAGAGGTTGATGATCTTAGTGACCGATTGTCACAACTTTTGGACACCATAGACCCTAACAGTGCTCAAGCAGCTATCATTAGGAGCTTACTTATGCAATAG
Protein sequence

>Msa1192100

MSSRRSRSRQSGVSTEISDAQINDLVTKLQQLVPELSRRSHKVSAAKVLQETCNYIKNLHREVDDLSDRLSQLLDTIDPNSAQAAIIRSLLMQ*