AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0640260

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0640260 MtrunA17_Chr4g0024181 86.486 74 10 0 1 74 1 74 7.35e-43 133
Msa0640260 MtrunA17_Chr2g0322831 70.000 50 15 0 24 73 30 79 4.20e-20 76.3
Msa0640260 MtrunA17_Chr5g0396771 65.217 46 16 0 26 71 37 82 5.23e-18 71.2
Msa0640260 MtrunA17_Chr2g0288361 49.333 75 35 2 1 73 1 74 5.52e-18 70.5
Msa0640260 MtrunA17_Chr7g0229101 57.143 42 18 0 27 68 29 70 4.82e-13 60.8
Msa0640260 MtrunA17_Chr4g0044421 58.537 41 17 0 28 68 70 110 1.12e-12 59.7
Msa0640260 MtrunA17_Chr4g0055981 63.415 41 15 0 28 68 113 153 2.50e-12 59.3
Msa0640260 MtrunA17_Chr4g0037141 58.537 41 17 0 28 68 70 110 2.81e-12 59.7
Msa0640260 MtrunA17_Chr8g0360111 58.537 41 17 0 28 68 83 123 3.51e-12 59.3
Msa0640260 MtrunA17_Chr5g0435101 56.098 41 18 0 28 68 69 109 3.67e-12 58.5
Msa0640260 MtrunA17_Chr7g0240821 54.545 44 20 0 28 71 59 102 4.51e-12 58.5
Msa0640260 MtrunA17_Chr3g0121241 57.143 42 18 0 27 68 99 140 6.00e-12 58.9
Msa0640260 MtrunA17_Chr4g0070641 58.537 41 17 0 28 68 70 110 7.60e-12 57.0
Msa0640260 MtrunA17_Chr4g0070611 57.500 40 16 1 29 68 72 110 1.16e-11 58.2
Msa0640260 MtrunA17_Chr8g0346561 56.098 41 18 0 28 68 70 110 2.21e-11 57.4
Msa0640260 MtrunA17_Chr7g0275911 57.143 42 17 1 30 71 73 113 2.21e-11 57.0
Msa0640260 MtrunA17_Chr7g0220341 56.098 41 18 0 28 68 85 125 2.24e-11 57.0
Msa0640260 MtrunA17_Chr3g0135311 50.000 42 21 0 28 69 71 112 6.42e-11 55.8
Msa0640260 MtrunA17_Chr1g0152011 52.381 42 20 0 28 69 71 112 6.45e-11 55.8
Msa0640260 MtrunA17_Chr5g0434901 51.220 41 20 0 28 68 31 71 7.00e-11 53.5
Msa0640260 MtrunA17_Chr7g0228991 51.220 41 20 0 28 68 87 127 8.19e-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
Msa0640260 AT2G46410.1 65.957 47 16 0 26 72 36 82 9.82e-17 68.2
Msa0640260 AT1G01380.1 68.293 41 13 0 26 66 32 72 1.40e-15 65.1
Msa0640260 AT5G53200.1 58.696 46 19 0 26 71 31 76 4.11e-14 62.0
Msa0640260 AT4G01060.3 63.415 41 15 0 26 66 31 71 9.21e-14 60.1
Msa0640260 AT4G01060.1 63.415 41 15 0 26 66 33 73 9.89e-14 60.1
Msa0640260 AT4G01060.2 63.415 41 15 0 26 66 30 70 9.92e-14 60.1
Msa0640260 AT2G30420.1 56.522 46 20 0 26 71 38 83 1.68e-12 58.2
Msa0640260 AT1G22640.3 58.537 41 17 0 28 68 13 53 3.07e-12 58.9
Msa0640260 AT4G38620.1 58.537 41 17 0 28 68 70 110 4.81e-12 59.3
Msa0640260 AT1G22640.1 58.537 41 17 0 28 68 70 110 6.62e-12 58.9
Msa0640260 AT5G14750.4 52.273 44 21 0 28 71 13 56 1.11e-11 56.6
Msa0640260 AT5G14750.2 52.273 44 21 0 28 71 13 56 1.11e-11 56.6
Msa0640260 AT5G35550.2 62.500 40 14 1 29 68 77 115 1.84e-11 57.8
Msa0640260 AT3G49690.1 54.762 42 19 0 28 69 71 112 1.89e-11 57.8
Msa0640260 AT4G09460.1 51.220 41 20 0 28 68 70 110 2.23e-11 57.0
Msa0640260 AT5G14750.3 52.273 44 21 0 28 71 40 83 2.24e-11 56.2
Msa0640260 AT3G27920.1 50.000 48 24 0 24 71 68 115 2.83e-11 57.0
Msa0640260 AT2G30424.1 48.077 52 24 1 26 74 34 85 3.01e-11 54.3
Msa0640260 AT3G13540.1 58.537 41 17 0 28 68 81 121 3.17e-11 57.0
Msa0640260 AT2G30432.1 52.174 46 22 0 26 71 33 78 3.68e-11 53.9
Msa0640260 AT5G14750.1 52.273 44 21 0 28 71 74 117 4.28e-11 56.2
Msa0640260 AT5G65790.1 52.381 42 20 0 28 69 71 112 6.48e-11 56.6

Find 27 sgRNAs with CRISPR-Local

Find 93 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ATCTCTTCTGCTGTTCTTCC+TGG 0.165221 4_3:+38432329 None:intergenic
AGAGGAAATGCTTATTAAAA+TGG 0.190572 4_3:-38432687 Msa0640260:CDS
ACTACAAATAGAGAAGAAAT+AGG 0.260769 4_3:+38433099 None:intergenic
AAATGGTTTATAATCTTGTT+GGG 0.339232 4_3:-38432670 Msa0640260:CDS
AAGTAAATTATTGTTAATAT+AGG 0.342014 4_3:+38433049 None:intergenic
TTGATTGCTGGAAGAATTCC+AGG 0.377394 4_3:-38432347 Msa0640260:CDS
TGAGTGGTGTATTAATATAT+AGG 0.379554 4_3:+38433023 None:intergenic
AAAATGGTTTATAATCTTGT+TGG 0.380870 4_3:-38432671 Msa0640260:CDS
CGTAGGTGGTCATTGATTGC+TGG 0.396538 4_3:-38432359 Msa0640260:intron
TTTCTTGATTCATTCATAGT+TGG 0.417658 4_3:+38432262 None:intergenic
TCAACCTTTGAACCTTGGTC+TGG 0.418134 4_3:+38432722 None:intergenic
AGAGAAGAAATAGGGAAGAC+GGG 0.426905 4_3:+38433108 None:intergenic
AATCAAGATGTGGGAAACTA+TGG 0.433656 4_3:+38432967 None:intergenic
CTACAAATAGAGAAGAAATA+GGG 0.442382 4_3:+38433100 None:intergenic
AAAATTCAACCTTTGAACCT+TGG 0.444402 4_3:+38432717 None:intergenic
GTATTTGATAATCAAGATGT+GGG 0.495195 4_3:+38432958 None:intergenic
TTTATAATCTTGTTGGGGAG+AGG 0.507013 4_3:-38432664 Msa0640260:intron
TGTATTTGATAATCAAGATG+TGG 0.524459 4_3:+38432957 None:intergenic
TGAATGAATCAAGAAATTTG+TGG 0.536313 4_3:-38432255 None:intergenic
AACTTAATTTGCTATTGCAA+TGG 0.540183 4_3:-38432919 Msa0640260:exon
TAGAGAAGAAATAGGGAAGA+CGG 0.548087 4_3:+38433107 None:intergenic
AATGGTTTATAATCTTGTTG+GGG 0.563787 4_3:-38432669 Msa0640260:CDS
GCAACCAGACCAAGGTTCAA+AGG 0.564494 4_3:-38432726 Msa0640260:CDS
AATGTTTCAACAGATTCCAA+AGG 0.613753 4_3:-38432873 Msa0640260:intron
GAGAAGAAATAGGGAAGACG+GGG 0.635275 4_3:+38433109 None:intergenic
ACAGATCAGCAACCAGACCA+AGG 0.650716 4_3:-38432734 Msa0640260:intron
TGAAATGATTGAGATTTGAG+TGG 0.677357 4_3:+38433007 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAGTAAATTATTGTTAATAT+AGG + chr4_3:38432330-38432349 None:intergenic 10.0%
!! AAGTAAATTATTGTTAATAT+AGG + chr4_3:38432330-38432349 None:intergenic 10.0%
!! AAGAAAAAAGTTACAATTTA+AGG + chr4_3:38432746-38432765 None:intergenic 15.0%
!! AAGAAAAAAGTTACAATTTA+AGG + chr4_3:38432746-38432765 None:intergenic 15.0%
!!! TGTCTTTTATAGCTAATTAA+TGG - chr4_3:38432543-38432562 Msa0640260:intron 20.0%
!! ATTTCTCTTAGTCAATAAAA+TGG + chr4_3:38432610-38432629 None:intergenic 20.0%
!!! ATTTTATTGACTAAGAGAAA+TGG - chr4_3:38432609-38432628 Msa0640260:intron 20.0%
!! AAAATGGTTTATAATCTTGT+TGG - chr4_3:38432705-38432724 Msa0640260:CDS 20.0%
!! AAATGGTTTATAATCTTGTT+GGG - chr4_3:38432706-38432725 Msa0640260:CDS 20.0%
!! ATAACATCAATAACAAAGTT+TGG + chr4_3:38432789-38432808 None:intergenic 20.0%
!! TATGAATGAATCAAGAAATT+TGG - chr4_3:38433119-38433138 Msa0640260:five_prime_UTR 20.0%
!!! TGTCTTTTATAGCTAATTAA+TGG - chr4_3:38432543-38432562 Msa0640260:intron 20.0%
!! ATTTCTCTTAGTCAATAAAA+TGG + chr4_3:38432610-38432629 None:intergenic 20.0%
!!! ATTTTATTGACTAAGAGAAA+TGG - chr4_3:38432609-38432628 Msa0640260:intron 20.0%
!! AAAATGGTTTATAATCTTGT+TGG - chr4_3:38432705-38432724 Msa0640260:CDS 20.0%
!! AAATGGTTTATAATCTTGTT+GGG - chr4_3:38432706-38432725 Msa0640260:CDS 20.0%
!! ATAACATCAATAACAAAGTT+TGG + chr4_3:38432789-38432808 None:intergenic 20.0%
! CTACAAATAGAGAAGAAATA+GGG + chr4_3:38432279-38432298 None:intergenic 25.0%
! ACTACAAATAGAGAAGAAAT+AGG + chr4_3:38432280-38432299 None:intergenic 25.0%
! TGAGTGGTGTATTAATATAT+AGG + chr4_3:38432356-38432375 None:intergenic 25.0%
!! GTATTTGATAATCAAGATGT+GGG + chr4_3:38432421-38432440 None:intergenic 25.0%
!! TGTATTTGATAATCAAGATG+TGG + chr4_3:38432422-38432441 None:intergenic 25.0%
!!! AACTTAATTTGCTATTGCAA+TGG - chr4_3:38432457-38432476 Msa0640260:intron 25.0%
!!! ATCTGTTGAAACATTTTTAG+AGG + chr4_3:38432498-38432517 None:intergenic 25.0%
! AAAAGACATGCATTCTAAAT+GGG + chr4_3:38432531-38432550 None:intergenic 25.0%
! TAAAAGACATGCATTCTAAA+TGG + chr4_3:38432532-38432551 None:intergenic 25.0%
! AGAGGAAATGCTTATTAAAA+TGG - chr4_3:38432689-38432708 Msa0640260:CDS 25.0%
! AATGGTTTATAATCTTGTTG+GGG - chr4_3:38432707-38432726 Msa0640260:CDS 25.0%
! CAGAAGAGATAGAAAAATAT+TGG - chr4_3:38433060-38433079 Msa0640260:five_prime_UTR 25.0%
! TTTCTTGATTCATTCATAGT+TGG + chr4_3:38433117-38433136 None:intergenic 25.0%
! CTACAAATAGAGAAGAAATA+GGG + chr4_3:38432279-38432298 None:intergenic 25.0%
! ACTACAAATAGAGAAGAAAT+AGG + chr4_3:38432280-38432299 None:intergenic 25.0%
! TGAGTGGTGTATTAATATAT+AGG + chr4_3:38432356-38432375 None:intergenic 25.0%
!! GTATTTGATAATCAAGATGT+GGG + chr4_3:38432421-38432440 None:intergenic 25.0%
!! TGTATTTGATAATCAAGATG+TGG + chr4_3:38432422-38432441 None:intergenic 25.0%
!!! AACTTAATTTGCTATTGCAA+TGG - chr4_3:38432457-38432476 Msa0640260:intron 25.0%
!!! ATCTGTTGAAACATTTTTAG+AGG + chr4_3:38432498-38432517 None:intergenic 25.0%
! AAAAGACATGCATTCTAAAT+GGG + chr4_3:38432531-38432550 None:intergenic 25.0%
! TAAAAGACATGCATTCTAAA+TGG + chr4_3:38432532-38432551 None:intergenic 25.0%
! AGAGGAAATGCTTATTAAAA+TGG - chr4_3:38432689-38432708 Msa0640260:CDS 25.0%
! AATGGTTTATAATCTTGTTG+GGG - chr4_3:38432707-38432726 Msa0640260:CDS 25.0%
! CAGAAGAGATAGAAAAATAT+TGG - chr4_3:38433060-38433079 Msa0640260:five_prime_UTR 25.0%
! TTTCTTGATTCATTCATAGT+TGG + chr4_3:38433117-38433136 None:intergenic 25.0%
TGAAATGATTGAGATTTGAG+TGG + chr4_3:38432372-38432391 None:intergenic 30.0%
AATGTTTCAACAGATTCCAA+AGG - chr4_3:38432503-38432522 Msa0640260:intron 30.0%
AAAATTCAACCTTTGAACCT+TGG + chr4_3:38432662-38432681 None:intergenic 30.0%
! TTTGGAATGAAAGTGAAAAG+AGG + chr4_3:38432771-38432790 None:intergenic 30.0%
GTCTAGTGTTTGTGTTTATT+TGG + chr4_3:38432825-38432844 None:intergenic 30.0%
! ATGAATGTGTATTTTCTCGT+AGG - chr4_3:38433000-38433019 Msa0640260:five_prime_UTR 30.0%
TGAAATGATTGAGATTTGAG+TGG + chr4_3:38432372-38432391 None:intergenic 30.0%
AATGTTTCAACAGATTCCAA+AGG - chr4_3:38432503-38432522 Msa0640260:intron 30.0%
AAAATTCAACCTTTGAACCT+TGG + chr4_3:38432662-38432681 None:intergenic 30.0%
! TTTGGAATGAAAGTGAAAAG+AGG + chr4_3:38432771-38432790 None:intergenic 30.0%
GTCTAGTGTTTGTGTTTATT+TGG + chr4_3:38432825-38432844 None:intergenic 30.0%
! ATGAATGTGTATTTTCTCGT+AGG - chr4_3:38433000-38433019 Msa0640260:five_prime_UTR 30.0%
TAGAGAAGAAATAGGGAAGA+CGG + chr4_3:38432272-38432291 None:intergenic 35.0%
AATCAAGATGTGGGAAACTA+TGG + chr4_3:38432412-38432431 None:intergenic 35.0%
!! GGTTGAATTTTCTGAAGAAG+AGG - chr4_3:38432671-38432690 Msa0640260:CDS 35.0%
TTTATAATCTTGTTGGGGAG+AGG - chr4_3:38432712-38432731 Msa0640260:CDS 35.0%
! AATGTGTATTTTCTCGTAGG+TGG - chr4_3:38433003-38433022 Msa0640260:five_prime_UTR 35.0%
TAGAGAAGAAATAGGGAAGA+CGG + chr4_3:38432272-38432291 None:intergenic 35.0%
AATCAAGATGTGGGAAACTA+TGG + chr4_3:38432412-38432431 None:intergenic 35.0%
!! GGTTGAATTTTCTGAAGAAG+AGG - chr4_3:38432671-38432690 Msa0640260:CDS 35.0%
TTTATAATCTTGTTGGGGAG+AGG - chr4_3:38432712-38432731 Msa0640260:CDS 35.0%
! AATGTGTATTTTCTCGTAGG+TGG - chr4_3:38433003-38433022 Msa0640260:five_prime_UTR 35.0%
AGAGAAGAAATAGGGAAGAC+GGG + chr4_3:38432271-38432290 None:intergenic 40.0%
GCATTCTAAATGGGTACCTT+TGG + chr4_3:38432522-38432541 None:intergenic 40.0%
AACACTGCATGTATTCCTGT+TGG - chr4_3:38432880-38432899 Msa0640260:CDS 40.0%
TACACATGTGAATGTCCAAC+AGG + chr4_3:38432898-38432917 None:intergenic 40.0%
! AAACCTTCGATCTAGAGTGT+CGG - chr4_3:38432929-38432948 Msa0640260:five_prime_UTR 40.0%
TTGATTGCTGGAAGAATTCC+AGG - chr4_3:38433029-38433048 Msa0640260:five_prime_UTR 40.0%
AGAGAAGAAATAGGGAAGAC+GGG + chr4_3:38432271-38432290 None:intergenic 40.0%
GCATTCTAAATGGGTACCTT+TGG + chr4_3:38432522-38432541 None:intergenic 40.0%
AACACTGCATGTATTCCTGT+TGG - chr4_3:38432880-38432899 Msa0640260:CDS 40.0%
TACACATGTGAATGTCCAAC+AGG + chr4_3:38432898-38432917 None:intergenic 40.0%
! AAACCTTCGATCTAGAGTGT+CGG - chr4_3:38432929-38432948 Msa0640260:five_prime_UTR 40.0%
TTGATTGCTGGAAGAATTCC+AGG - chr4_3:38433029-38433048 Msa0640260:five_prime_UTR 40.0%
GAGAAGAAATAGGGAAGACG+GGG + chr4_3:38432270-38432289 None:intergenic 45.0%
TCAACCTTTGAACCTTGGTC+TGG + chr4_3:38432657-38432676 None:intergenic 45.0%
CTCTAGATCGAAGGTTTGTC+TGG + chr4_3:38432926-38432945 None:intergenic 45.0%
ATCTCTTCTGCTGTTCTTCC+TGG + chr4_3:38433050-38433069 None:intergenic 45.0%
GAGAAGAAATAGGGAAGACG+GGG + chr4_3:38432270-38432289 None:intergenic 45.0%
TCAACCTTTGAACCTTGGTC+TGG + chr4_3:38432657-38432676 None:intergenic 45.0%
CTCTAGATCGAAGGTTTGTC+TGG + chr4_3:38432926-38432945 None:intergenic 45.0%
ATCTCTTCTGCTGTTCTTCC+TGG + chr4_3:38433050-38433069 None:intergenic 45.0%
ACAGATCAGCAACCAGACCA+AGG - chr4_3:38432642-38432661 Msa0640260:intron 50.0%
GCAACCAGACCAAGGTTCAA+AGG - chr4_3:38432650-38432669 Msa0640260:intron 50.0%
ACACCGACACTCTAGATCGA+AGG + chr4_3:38432935-38432954 None:intergenic 50.0%
! CGTAGGTGGTCATTGATTGC+TGG - chr4_3:38433017-38433036 Msa0640260:five_prime_UTR 50.0%
ACAGATCAGCAACCAGACCA+AGG - chr4_3:38432642-38432661 Msa0640260:intron 50.0%
GCAACCAGACCAAGGTTCAA+AGG - chr4_3:38432650-38432669 Msa0640260:intron 50.0%
ACACCGACACTCTAGATCGA+AGG + chr4_3:38432935-38432954 None:intergenic 50.0%
! CGTAGGTGGTCATTGATTGC+TGG - chr4_3:38433017-38433036 Msa0640260:five_prime_UTR 50.0%
Chromosome Type Strat End Strand Name
chr4_3 gene 38432258 38433140 38432258 ID=Msa0640260;Name=Msa0640260
chr4_3 mRNA 38432258 38433140 38432258 ID=Msa0640260-mRNA-1;Parent=Msa0640260;Name=Msa0640260-mRNA-1;_AED=0.02;_eAED=0.02;_QI=218|1|1|1|1|1|3|31|74
chr4_3 exon 38432258 38432376 38432258 ID=Msa0640260-mRNA-1:exon:8681;Parent=Msa0640260-mRNA-1
chr4_3 exon 38432665 38432752 38432665 ID=Msa0640260-mRNA-1:exon:8680;Parent=Msa0640260-mRNA-1
chr4_3 exon 38432874 38433140 38432874 ID=Msa0640260-mRNA-1:exon:8679;Parent=Msa0640260-mRNA-1
chr4_3 five_prime_UTR 38432923 38433140 38432923 ID=Msa0640260-mRNA-1:five_prime_utr;Parent=Msa0640260-mRNA-1
chr4_3 CDS 38432874 38432922 38432874 ID=Msa0640260-mRNA-1:cds;Parent=Msa0640260-mRNA-1
chr4_3 CDS 38432665 38432752 38432665 ID=Msa0640260-mRNA-1:cds;Parent=Msa0640260-mRNA-1
chr4_3 CDS 38432289 38432376 38432289 ID=Msa0640260-mRNA-1:cds;Parent=Msa0640260-mRNA-1
chr4_3 three_prime_UTR 38432258 38432288 38432258 ID=Msa0640260-mRNA-1:three_prime_utr;Parent=Msa0640260-mRNA-1
Gene Sequence

>Msa0640260

ATGGCTGACTCAGAACACTCCTCTAAAAATGTTTCAACAGATTCCAAAGATCAGCAACCAGACCAAGGTTCAAAGGTTGAATTTTCTGAAGAAGAGGAAATGCTTATTAAAATGGTTTATAATCTTGTTGGGGAGAGGTGGTCATTGATTGCTGGAAGAATTCCAGGAAGAACAGCAGAAGAGATAGAAAAATATTGGAATTCAAGACACTCGACTAGCAAATGA
Protein sequence

>Msa0640260

MADSEHSSKNVSTDSKDQQPDQGSKVEFSEEEEMLIKMVYNLVGERWSLIAGRIPGRTAEEIEKYWNSRHSTSK*