AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0599560

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0599560 MtrunA17_Chr4g0024181 86.486 74 10 0 1 74 1 74 4.38e-43 134
Msa0599560 MtrunA17_Chr2g0322831 70.000 50 15 0 24 73 30 79 6.30e-20 75.5
Msa0599560 MtrunA17_Chr5g0396771 51.429 70 25 2 10 71 14 82 2.23e-18 72.0
Msa0599560 MtrunA17_Chr2g0288361 49.333 75 35 2 1 73 1 74 1.17e-17 69.7
Msa0599560 MtrunA17_Chr7g0229101 57.143 42 18 0 27 68 29 70 5.35e-13 60.8
Msa0599560 MtrunA17_Chr4g0044421 58.537 41 17 0 28 68 70 110 1.24e-12 59.7
Msa0599560 MtrunA17_Chr4g0055981 63.415 41 15 0 28 68 113 153 2.80e-12 59.3
Msa0599560 MtrunA17_Chr4g0037141 58.537 41 17 0 28 68 70 110 2.95e-12 59.7
Msa0599560 MtrunA17_Chr8g0360111 58.537 41 17 0 28 68 83 123 3.97e-12 58.9
Msa0599560 MtrunA17_Chr5g0435101 56.098 41 18 0 28 68 69 109 4.20e-12 58.5
Msa0599560 MtrunA17_Chr7g0240821 54.545 44 20 0 28 71 59 102 5.15e-12 58.5
Msa0599560 MtrunA17_Chr3g0121241 55.556 45 20 0 27 71 99 143 7.18e-12 58.5
Msa0599560 MtrunA17_Chr4g0070641 58.537 41 17 0 28 68 70 110 8.10e-12 57.0
Msa0599560 MtrunA17_Chr4g0070611 57.500 40 16 1 29 68 72 110 1.30e-11 57.8
Msa0599560 MtrunA17_Chr8g0346561 56.098 41 18 0 28 68 70 110 2.34e-11 57.0
Msa0599560 MtrunA17_Chr7g0220341 56.098 41 18 0 28 68 85 125 2.40e-11 57.0
Msa0599560 MtrunA17_Chr7g0275911 57.143 42 17 1 30 71 73 113 2.42e-11 57.0
Msa0599560 MtrunA17_Chr3g0135311 50.000 42 21 0 28 69 71 112 6.18e-11 56.2
Msa0599560 MtrunA17_Chr1g0152011 52.381 42 20 0 28 69 71 112 6.64e-11 55.8
Msa0599560 MtrunA17_Chr5g0434901 51.220 41 20 0 28 68 31 71 7.79e-11 53.5
Msa0599560 MtrunA17_Chr7g0228991 51.220 41 20 0 28 68 87 127 8.96e-11 55.5
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0599560 AT2G46410.1 65.957 47 16 0 26 72 36 82 1.26e-16 68.2
Msa0599560 AT1G01380.1 68.293 41 13 0 26 66 32 72 1.67e-15 64.7
Msa0599560 AT5G53200.1 58.696 46 19 0 26 71 31 76 5.64e-14 61.6
Msa0599560 AT4G01060.3 63.415 41 15 0 26 66 31 71 9.84e-14 60.1
Msa0599560 AT4G01060.1 63.415 41 15 0 26 66 33 73 1.17e-13 60.1
Msa0599560 AT4G01060.2 63.415 41 15 0 26 66 30 70 1.18e-13 60.1
Msa0599560 AT2G30420.1 56.522 46 20 0 26 71 38 83 1.59e-12 58.2
Msa0599560 AT1G22640.3 58.537 41 17 0 28 68 13 53 3.34e-12 58.9
Msa0599560 AT4G38620.1 58.537 41 17 0 28 68 70 110 4.86e-12 59.3
Msa0599560 AT1G22640.1 58.537 41 17 0 28 68 70 110 7.04e-12 58.5
Msa0599560 AT5G14750.4 52.273 44 21 0 28 71 13 56 1.18e-11 56.6
Msa0599560 AT5G14750.2 52.273 44 21 0 28 71 13 56 1.18e-11 56.6
Msa0599560 AT5G35550.2 62.500 40 14 1 29 68 77 115 1.56e-11 57.8
Msa0599560 AT3G49690.1 54.762 42 19 0 28 69 71 112 1.98e-11 57.8
Msa0599560 AT4G09460.1 51.220 41 20 0 28 68 70 110 2.27e-11 57.0
Msa0599560 AT5G14750.3 52.273 44 21 0 28 71 40 83 2.29e-11 56.2
Msa0599560 AT2G30424.1 39.189 74 42 1 4 74 12 85 2.43e-11 54.7
Msa0599560 AT3G27920.1 50.000 48 24 0 24 71 68 115 2.80e-11 57.0
Msa0599560 AT3G13540.1 58.537 41 17 0 28 68 81 121 3.10e-11 57.0
Msa0599560 AT2G30432.1 52.174 46 22 0 26 71 33 78 3.30e-11 53.9
Msa0599560 AT5G14750.1 52.273 44 21 0 28 71 74 117 4.42e-11 55.8
Msa0599560 AT5G65790.1 52.381 42 20 0 28 69 71 112 6.54e-11 56.2

Find 28 sgRNAs with CRISPR-Local

Find 97 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AGAGGAAATGCTTATTAAAA+TGG 0.190572 4_2:-39376841 Msa0599560:CDS
ATCTCTTCTGCTGTTCTTCC+AGG 0.213845 4_2:+39376454 None:intergenic
ACTACAAATAGAGAAGAAAT+AGG 0.260769 4_2:+39377254 None:intergenic
AAAAGGGTACCTTTGGAATC+TGG 0.327443 4_2:+39377018 None:intergenic
AAATGGTTTATAATCTTGTT+GGG 0.339232 4_2:-39376824 Msa0599560:CDS
AAGTAAATTATTGTTAATAT+AGG 0.342014 4_2:+39377204 None:intergenic
TTGATTGCTGGAAGAATTCC+TGG 0.342209 4_2:-39376472 Msa0599560:CDS
TGAGTGGTGTATTAATATAT+AGG 0.379554 4_2:+39377178 None:intergenic
AAAATGGTTTATAATCTTGT+TGG 0.380870 4_2:-39376825 Msa0599560:CDS
CATAGGTGGTCATTGATTGC+TGG 0.399125 4_2:-39376484 Msa0599560:intron
TTTCTTGATTCATTCATAGT+TGG 0.417658 4_2:+39376387 None:intergenic
TCAACCTTTGAACCTTGGTC+TGG 0.418134 4_2:+39376876 None:intergenic
AGAGAAGAAATAGGGAAGAC+GGG 0.426905 4_2:+39377263 None:intergenic
AATCAAGATGTGGGAAACTA+TGG 0.433656 4_2:+39377122 None:intergenic
CTACAAATAGAGAAGAAATA+GGG 0.442382 4_2:+39377255 None:intergenic
AAAATTCAACCTTTGAACCT+TGG 0.444402 4_2:+39376871 None:intergenic
TTTATAATCTTGTTGGGGAG+AGG 0.507013 4_2:-39376818 Msa0599560:intron
ACTTAATTTGCTATTTGCAA+TGG 0.515447 4_2:-39377073 Msa0599560:exon
CTATTTGATAATCAAGATGT+GGG 0.528349 4_2:+39377113 None:intergenic
TCTATTTGATAATCAAGATG+TGG 0.534329 4_2:+39377112 None:intergenic
TGAATGAATCAAGAAATTTG+TGG 0.536313 4_2:-39376380 None:intergenic
TAGAGAAGAAATAGGGAAGA+CGG 0.548087 4_2:+39377262 None:intergenic
AATGGTTTATAATCTTGTTG+GGG 0.563787 4_2:-39376823 Msa0599560:CDS
GCAACCAGACCAAGGTTCAA+AGG 0.564494 4_2:-39376880 Msa0599560:CDS
AATGTTTCACCAGATTCCAA+AGG 0.629431 4_2:-39377027 Msa0599560:intron
GAGAAGAAATAGGGAAGACG+GGG 0.635275 4_2:+39377264 None:intergenic
ACAGATCAGCAACCAGACCA+AGG 0.650716 4_2:-39376888 Msa0599560:intron
TGGAATGATTGAGATTTGAG+TGG 0.693035 4_2:+39377162 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAGTAAATTATTGTTAATAT+AGG + chr4_2:39376455-39376474 None:intergenic 10.0%
!! TAAAAAAAAGTTACAATTTA+AGG + chr4_2:39376872-39376891 None:intergenic 10.0%
!! AAGTAAATTATTGTTAATAT+AGG + chr4_2:39376455-39376474 None:intergenic 10.0%
!! TAAAAAAAAGTTACAATTTA+AGG + chr4_2:39376872-39376891 None:intergenic 10.0%
!!! TGTCTTTTATAGCTAATTAA+TGG - chr4_2:39376669-39376688 Msa0599560:intron 20.0%
!! ATTTCTCTTAGTCAATAAAA+TGG + chr4_2:39376736-39376755 None:intergenic 20.0%
!!! ATTTTATTGACTAAGAGAAA+TGG - chr4_2:39376735-39376754 Msa0599560:intron 20.0%
!! AAAATGGTTTATAATCTTGT+TGG - chr4_2:39376831-39376850 Msa0599560:CDS 20.0%
!! AAATGGTTTATAATCTTGTT+GGG - chr4_2:39376832-39376851 Msa0599560:CDS 20.0%
!! ATAACATCAATAACAAAGTT+TGG + chr4_2:39376913-39376932 None:intergenic 20.0%
!! TATGAATGAATCAAGAAATT+TGG - chr4_2:39377274-39377293 Msa0599560:five_prime_UTR 20.0%
!!! TGTCTTTTATAGCTAATTAA+TGG - chr4_2:39376669-39376688 Msa0599560:intron 20.0%
!! ATTTCTCTTAGTCAATAAAA+TGG + chr4_2:39376736-39376755 None:intergenic 20.0%
!!! ATTTTATTGACTAAGAGAAA+TGG - chr4_2:39376735-39376754 Msa0599560:intron 20.0%
!! AAAATGGTTTATAATCTTGT+TGG - chr4_2:39376831-39376850 Msa0599560:CDS 20.0%
!! AAATGGTTTATAATCTTGTT+GGG - chr4_2:39376832-39376851 Msa0599560:CDS 20.0%
!! ATAACATCAATAACAAAGTT+TGG + chr4_2:39376913-39376932 None:intergenic 20.0%
! CTACAAATAGAGAAGAAATA+GGG + chr4_2:39376404-39376423 None:intergenic 25.0%
! ACTACAAATAGAGAAGAAAT+AGG + chr4_2:39376405-39376424 None:intergenic 25.0%
! TGAGTGGTGTATTAATATAT+AGG + chr4_2:39376481-39376500 None:intergenic 25.0%
!! CTATTTGATAATCAAGATGT+GGG + chr4_2:39376546-39376565 None:intergenic 25.0%
!! TCTATTTGATAATCAAGATG+TGG + chr4_2:39376547-39376566 None:intergenic 25.0%
!!! ACTTAATTTGCTATTTGCAA+TGG - chr4_2:39376583-39376602 Msa0599560:intron 25.0%
!! AAAAGACATGCATTCTAAAA+GGG + chr4_2:39376657-39376676 None:intergenic 25.0%
! TAAAAGACATGCATTCTAAA+AGG + chr4_2:39376658-39376677 None:intergenic 25.0%
! AGAGGAAATGCTTATTAAAA+TGG - chr4_2:39376815-39376834 Msa0599560:intron 25.0%
! AATGGTTTATAATCTTGTTG+GGG - chr4_2:39376833-39376852 Msa0599560:CDS 25.0%
!! ATGAATGTGTATTTTCTCAT+AGG - chr4_2:39377155-39377174 Msa0599560:five_prime_UTR 25.0%
! CAGAAGAGATAGAAAAATAT+TGG - chr4_2:39377215-39377234 Msa0599560:five_prime_UTR 25.0%
! TTTCTTGATTCATTCATAGT+TGG + chr4_2:39377272-39377291 None:intergenic 25.0%
! CTACAAATAGAGAAGAAATA+GGG + chr4_2:39376404-39376423 None:intergenic 25.0%
! ACTACAAATAGAGAAGAAAT+AGG + chr4_2:39376405-39376424 None:intergenic 25.0%
! TGAGTGGTGTATTAATATAT+AGG + chr4_2:39376481-39376500 None:intergenic 25.0%
!! CTATTTGATAATCAAGATGT+GGG + chr4_2:39376546-39376565 None:intergenic 25.0%
!! TCTATTTGATAATCAAGATG+TGG + chr4_2:39376547-39376566 None:intergenic 25.0%
!!! ACTTAATTTGCTATTTGCAA+TGG - chr4_2:39376583-39376602 Msa0599560:intron 25.0%
!! AAAAGACATGCATTCTAAAA+GGG + chr4_2:39376657-39376676 None:intergenic 25.0%
! TAAAAGACATGCATTCTAAA+AGG + chr4_2:39376658-39376677 None:intergenic 25.0%
! AGAGGAAATGCTTATTAAAA+TGG - chr4_2:39376815-39376834 Msa0599560:intron 25.0%
! AATGGTTTATAATCTTGTTG+GGG - chr4_2:39376833-39376852 Msa0599560:CDS 25.0%
!! ATGAATGTGTATTTTCTCAT+AGG - chr4_2:39377155-39377174 Msa0599560:five_prime_UTR 25.0%
! CAGAAGAGATAGAAAAATAT+TGG - chr4_2:39377215-39377234 Msa0599560:five_prime_UTR 25.0%
! TTTCTTGATTCATTCATAGT+TGG + chr4_2:39377272-39377291 None:intergenic 25.0%
!!! TGGTGTTATTTTGCAGAATA+TGG + chr4_2:39376517-39376536 None:intergenic 30.0%
!! ATCTGGTGAAACATTTTTAG+AGG + chr4_2:39376624-39376643 None:intergenic 30.0%
AAAATTCAACCTTTGAACCT+TGG + chr4_2:39376788-39376807 None:intergenic 30.0%
! TTTGGAATGAAAGTGAAAAG+AGG + chr4_2:39376895-39376914 None:intergenic 30.0%
GTCTAGTGTTTGTGTTTATT+TGG + chr4_2:39376949-39376968 None:intergenic 30.0%
! AATGTGTATTTTCTCATAGG+TGG - chr4_2:39377158-39377177 Msa0599560:five_prime_UTR 30.0%
!!! TGGTGTTATTTTGCAGAATA+TGG + chr4_2:39376517-39376536 None:intergenic 30.0%
!! ATCTGGTGAAACATTTTTAG+AGG + chr4_2:39376624-39376643 None:intergenic 30.0%
AAAATTCAACCTTTGAACCT+TGG + chr4_2:39376788-39376807 None:intergenic 30.0%
! TTTGGAATGAAAGTGAAAAG+AGG + chr4_2:39376895-39376914 None:intergenic 30.0%
GTCTAGTGTTTGTGTTTATT+TGG + chr4_2:39376949-39376968 None:intergenic 30.0%
! AATGTGTATTTTCTCATAGG+TGG - chr4_2:39377158-39377177 Msa0599560:five_prime_UTR 30.0%
TAGAGAAGAAATAGGGAAGA+CGG + chr4_2:39376397-39376416 None:intergenic 35.0%
TGGAATGATTGAGATTTGAG+TGG + chr4_2:39376497-39376516 None:intergenic 35.0%
AATCAAGATGTGGGAAACTA+TGG + chr4_2:39376537-39376556 None:intergenic 35.0%
AATGTTTCACCAGATTCCAA+AGG - chr4_2:39376629-39376648 Msa0599560:intron 35.0%
!! GGTTGAATTTTCTGAAGAAG+AGG - chr4_2:39376797-39376816 Msa0599560:intron 35.0%
TTTATAATCTTGTTGGGGAG+AGG - chr4_2:39376838-39376857 Msa0599560:CDS 35.0%
TAGAGAAGAAATAGGGAAGA+CGG + chr4_2:39376397-39376416 None:intergenic 35.0%
TGGAATGATTGAGATTTGAG+TGG + chr4_2:39376497-39376516 None:intergenic 35.0%
AATCAAGATGTGGGAAACTA+TGG + chr4_2:39376537-39376556 None:intergenic 35.0%
AATGTTTCACCAGATTCCAA+AGG - chr4_2:39376629-39376648 Msa0599560:intron 35.0%
!! GGTTGAATTTTCTGAAGAAG+AGG - chr4_2:39376797-39376816 Msa0599560:intron 35.0%
TTTATAATCTTGTTGGGGAG+AGG - chr4_2:39376838-39376857 Msa0599560:CDS 35.0%
AGAGAAGAAATAGGGAAGAC+GGG + chr4_2:39376396-39376415 None:intergenic 40.0%
!! AAAAGGGTACCTTTGGAATC+TGG + chr4_2:39376641-39376660 None:intergenic 40.0%
!! GCATTCTAAAAGGGTACCTT+TGG + chr4_2:39376648-39376667 None:intergenic 40.0%
AACACTGCATGTATTCCTGT+TGG - chr4_2:39377035-39377054 Msa0599560:CDS 40.0%
TACACATGTGAATGTCCAAC+AGG + chr4_2:39377053-39377072 None:intergenic 40.0%
! AAACCTTCGATCTAGAGTGT+CGG - chr4_2:39377084-39377103 Msa0599560:five_prime_UTR 40.0%
TTGATTGCTGGAAGAATTCC+TGG - chr4_2:39377184-39377203 Msa0599560:five_prime_UTR 40.0%
AGAGAAGAAATAGGGAAGAC+GGG + chr4_2:39376396-39376415 None:intergenic 40.0%
!! AAAAGGGTACCTTTGGAATC+TGG + chr4_2:39376641-39376660 None:intergenic 40.0%
!! GCATTCTAAAAGGGTACCTT+TGG + chr4_2:39376648-39376667 None:intergenic 40.0%
AACACTGCATGTATTCCTGT+TGG - chr4_2:39377035-39377054 Msa0599560:CDS 40.0%
TACACATGTGAATGTCCAAC+AGG + chr4_2:39377053-39377072 None:intergenic 40.0%
! AAACCTTCGATCTAGAGTGT+CGG - chr4_2:39377084-39377103 Msa0599560:five_prime_UTR 40.0%
TTGATTGCTGGAAGAATTCC+TGG - chr4_2:39377184-39377203 Msa0599560:five_prime_UTR 40.0%
GAGAAGAAATAGGGAAGACG+GGG + chr4_2:39376395-39376414 None:intergenic 45.0%
TCAACCTTTGAACCTTGGTC+TGG + chr4_2:39376783-39376802 None:intergenic 45.0%
CTCTAGATCGAAGGTTTGTC+TGG + chr4_2:39377081-39377100 None:intergenic 45.0%
! CATAGGTGGTCATTGATTGC+TGG - chr4_2:39377172-39377191 Msa0599560:five_prime_UTR 45.0%
ATCTCTTCTGCTGTTCTTCC+AGG + chr4_2:39377205-39377224 None:intergenic 45.0%
GAGAAGAAATAGGGAAGACG+GGG + chr4_2:39376395-39376414 None:intergenic 45.0%
TCAACCTTTGAACCTTGGTC+TGG + chr4_2:39376783-39376802 None:intergenic 45.0%
CTCTAGATCGAAGGTTTGTC+TGG + chr4_2:39377081-39377100 None:intergenic 45.0%
! CATAGGTGGTCATTGATTGC+TGG - chr4_2:39377172-39377191 Msa0599560:five_prime_UTR 45.0%
ATCTCTTCTGCTGTTCTTCC+AGG + chr4_2:39377205-39377224 None:intergenic 45.0%
ACAGATCAGCAACCAGACCA+AGG - chr4_2:39376768-39376787 Msa0599560:intron 50.0%
GCAACCAGACCAAGGTTCAA+AGG - chr4_2:39376776-39376795 Msa0599560:intron 50.0%
ACACCGACACTCTAGATCGA+AGG + chr4_2:39377090-39377109 None:intergenic 50.0%
ACAGATCAGCAACCAGACCA+AGG - chr4_2:39376768-39376787 Msa0599560:intron 50.0%
GCAACCAGACCAAGGTTCAA+AGG - chr4_2:39376776-39376795 Msa0599560:intron 50.0%
ACACCGACACTCTAGATCGA+AGG + chr4_2:39377090-39377109 None:intergenic 50.0%
Chromosome Type Strat End Strand Name
chr4_2 gene 39376383 39377295 39376383 ID=Msa0599560;Name=Msa0599560
chr4_2 mRNA 39376383 39377295 39376383 ID=Msa0599560-mRNA-1;Parent=Msa0599560;Name=Msa0599560-mRNA-1;_AED=0.02;_eAED=0.02;_QI=219|1|1|1|1|1|3|31|74
chr4_2 exon 39376383 39376501 39376383 ID=Msa0599560-mRNA-1:exon:8606;Parent=Msa0599560-mRNA-1
chr4_2 exon 39376819 39376906 39376819 ID=Msa0599560-mRNA-1:exon:8605;Parent=Msa0599560-mRNA-1
chr4_2 exon 39377028 39377295 39377028 ID=Msa0599560-mRNA-1:exon:8604;Parent=Msa0599560-mRNA-1
chr4_2 five_prime_UTR 39377077 39377295 39377077 ID=Msa0599560-mRNA-1:five_prime_utr;Parent=Msa0599560-mRNA-1
chr4_2 CDS 39377028 39377076 39377028 ID=Msa0599560-mRNA-1:cds;Parent=Msa0599560-mRNA-1
chr4_2 CDS 39376819 39376906 39376819 ID=Msa0599560-mRNA-1:cds;Parent=Msa0599560-mRNA-1
chr4_2 CDS 39376414 39376501 39376414 ID=Msa0599560-mRNA-1:cds;Parent=Msa0599560-mRNA-1
chr4_2 three_prime_UTR 39376383 39376413 39376383 ID=Msa0599560-mRNA-1:three_prime_utr;Parent=Msa0599560-mRNA-1
Gene Sequence

>Msa0599560

ATGGCTGACTCAGAACACTCCTCTAAAAATGTTTCACCAGATTCCAAAGATCAGCAACCAGACCAAGGTTCAAAGGTTGAATTTTCTGAAGAAGAGGAAATGCTTATTAAAATGGTTTATAATCTTGTTGGGGAGAGGTGGTCATTGATTGCTGGAAGAATTCCTGGAAGAACAGCAGAAGAGATAGAAAAATATTGGAATTCAAGACACTCGACTAGCAAATGA
Protein sequence

>Msa0599560

MADSEHSSKNVSPDSKDQQPDQGSKVEFSEEEEMLIKMVYNLVGERWSLIAGRIPGRTAEEIEKYWNSRHSTSK*