AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0978630

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0978630 MtrunA17_Chr6g0457521 50.365 137 50 5 1 130 49 174 1.48e-25 97.1
Msa0978630 MtrunA17_Chr6g0460421 56.250 80 27 2 9 86 2 75 9.05e-20 85.5
Msa0978630 MtrunA17_Chr6g0457551 85.366 41 6 0 9 49 2 42 1.93e-19 77.8
Msa0978630 MtrunA17_Chr1g0146381 66.667 51 17 0 6 56 2 52 2.84e-19 78.2
Msa0978630 MtrunA17_Chr6g0457541 85.106 47 6 1 11 56 4 50 2.62e-18 81.3
Msa0978630 MtrunA17_Chr6g0460451 57.692 78 29 2 9 86 2 75 5.63e-18 80.5
Msa0978630 MtrunA17_Chr3g0088921 74.510 51 13 0 7 57 1 51 6.53e-18 80.5
Msa0978630 MtrunA17_Chr6g0457531 57.971 69 29 0 9 77 2 70 8.61e-18 80.1
Msa0978630 MtrunA17_Chr3g0088671 77.778 45 10 0 9 53 2 46 2.46e-17 78.6
Msa0978630 MtrunA17_Chr3g0088571 70.833 48 14 0 9 56 2 49 3.41e-17 75.1
Msa0978630 MtrunA17_Chr3g0088741 59.155 71 25 2 9 75 2 72 4.68e-17 77.8
Msa0978630 MtrunA17_Chr3g0088601 50.000 86 42 1 6 91 11 95 8.30e-17 77.4
Msa0978630 MtrunA17_Chr2g0303111 74.468 47 12 0 7 53 1 47 9.02e-17 77.0
Msa0978630 MtrunA17_Chr3g0088651 75.000 44 11 0 9 52 2 45 9.05e-17 74.3
Msa0978630 MtrunA17_Chr3g0088691 75.000 44 11 0 9 52 2 45 1.23e-16 73.9
Msa0978630 MtrunA17_Chr6g0457501 70.833 48 14 0 9 56 2 49 4.59e-16 75.5
Msa0978630 MtrunA17_Chr3g0088551 72.917 48 13 0 9 56 2 49 4.71e-16 75.1
Msa0978630 MtrunA17_Chr1g0157711 48.649 74 36 1 7 78 1 74 1.41e-15 73.6
Msa0978630 MtrunA17_Chr3g0088951 70.000 50 14 1 9 57 2 51 2.68e-15 72.8
Msa0978630 MtrunA17_Chr3g0088721 62.000 50 19 0 4 53 1 50 2.82e-15 72.8
Msa0978630 MtrunA17_Chr3g0088591 47.436 78 33 1 6 83 15 84 3.25e-15 70.1
Msa0978630 MtrunA17_Chr3g0088631 56.452 62 27 0 9 70 2 63 6.53e-15 72.0
Msa0978630 MtrunA17_Chr3g0088621 46.753 77 33 1 8 84 12 80 2.31e-14 70.5
Msa0978630 MtrunA17_Chr3g0088991 55.224 67 19 2 7 62 1 67 4.47e-14 69.3
Msa0978630 MtrunA17_Chr3g0089001 55.385 65 18 2 9 62 32 96 1.59e-13 67.8
Msa0978630 MtrunA17_Chr3g0088841 66.667 48 15 1 7 53 1 48 2.00e-13 67.8
Msa0978630 MtrunA17_Chr3g0127321 65.306 49 16 1 6 53 28 76 3.02e-13 67.4
Msa0978630 MtrunA17_Chr3g0088701 56.667 60 25 1 4 63 1 59 3.09e-13 67.0
Msa0978630 MtrunA17_Chr1g0151721 53.425 73 23 2 5 67 14 85 3.26e-13 67.0
Msa0978630 MtrunA17_Chr3g0088751 64.583 48 16 1 9 56 2 48 3.91e-13 66.6
Msa0978630 MtrunA17_Chr3g0088661 56.667 60 25 1 4 63 1 59 6.00e-13 65.9
Msa0978630 MtrunA17_Chr3g0088931 64.583 48 16 1 11 57 4 51 9.36e-13 65.9
Msa0978630 MtrunA17_Chr1g0146401 49.296 71 32 1 11 77 21 91 2.91e-12 64.3
Msa0978630 MtrunA17_Chr3g0088541 66.667 42 14 0 10 51 2 43 6.23e-12 63.2
Msa0978630 MtrunA17_Chr3g0127311 59.574 47 19 0 7 53 2 48 7.18e-12 63.2
Msa0978630 MtrunA17_Chr3g0088831 40.000 85 39 2 3 87 7 79 1.39e-11 62.4
Msa0978630 MtrunA17_Chr1g0170781 68.293 41 13 0 5 45 12 52 1.47e-11 62.4
Msa0978630 MtrunA17_Chr7g0214521 62.000 50 17 2 8 55 8 57 2.27e-11 61.6
Msa0978630 MtrunA17_Chr3g0088531 50.847 59 28 1 12 70 3 60 4.22e-11 60.8
Msa0978630 MtrunA17_Chr3g0101901 60.465 43 17 0 5 47 19 61 4.97e-11 58.5
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 43 sgRNAs with CRISPR-Local

Find 64 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AAAATTATCTCTCCTCCATT+TGG 0.305378 6_4:-14662994 Msa0978630:CDS
TTTGTTGTTGTTCTTGTTGT+TGG 0.348750 6_4:+14663135 None:intergenic
AAATTATCTCTCCTCCATTT+GGG 0.404433 6_4:-14662993 Msa0978630:CDS
GAAGGGTTGATGTTGGGAAT+AGG 0.430716 6_4:+14662941 None:intergenic
TTATCAACCAAGGGCGAAGT+AGG 0.446707 6_4:+14663111 None:intergenic
ACTATTGAAGGGTTGATGTT+GGG 0.454182 6_4:+14662935 None:intergenic
AACAAACCCTACTTCGCCCT+TGG 0.463083 6_4:-14663118 Msa0978630:intron
TGACTACATGTTCCCTGAAA+AGG 0.470098 6_4:-14662913 Msa0978630:CDS
GAACATGTAGTCACTATTGA+AGG 0.476485 6_4:+14662923 None:intergenic
GTCGTTGCTGTCACGTGCCA+TGG 0.491026 6_4:-14662891 Msa0978630:CDS
CACTATTGAAGGGTTGATGT+TGG 0.495406 6_4:+14662934 None:intergenic
TCAGATTGAGAAGGTCTGTT+GGG 0.508699 6_4:+14663366 None:intergenic
TGAAAGTGTTGCTTCCCAAA+TGG 0.510671 6_4:+14662979 None:intergenic
TGTTCTTGTTGTTGGTGTGG+TGG 0.515272 6_4:+14663143 None:intergenic
TGTTTGGAGAGGTGACAGAA+TGG 0.519350 6_4:+14663185 None:intergenic
TCCGTTCAATTTGTTCAACA+TGG 0.529209 6_4:-14663304 Msa0978630:CDS
CCAGTCGACAGCCGCTGCCA+TGG 0.531422 6_4:+14663397 None:intergenic
ATCAGATTGAGAAGGTCTGT+TGG 0.532634 6_4:+14663365 None:intergenic
TTGGAGAGGTGACAGAATGG+AGG 0.540854 6_4:+14663188 None:intergenic
TGGGAAGCAACACTTTCACT+AGG 0.545995 6_4:-14662974 Msa0978630:CDS
CAGTAACGGCTCTGGGTGAG+AGG 0.548246 6_4:+14662839 None:intergenic
TGTTGTTCTTGTTGTTGGTG+TGG 0.559442 6_4:+14663140 None:intergenic
GAGGGGAATCACAGAAAAGT+GGG 0.560445 6_4:+14663048 None:intergenic
TGGAGAGGTGACAGAATGGA+GGG 0.561195 6_4:+14663189 None:intergenic
ATGAGACTGATACGAGGAAG+AGG 0.565004 6_4:+14663029 None:intergenic
TATCAACCAAGGGCGAAGTA+GGG 0.568592 6_4:+14663112 None:intergenic
AGAGGGGAATCACAGAAAAG+TGG 0.571573 6_4:+14663047 None:intergenic
GTTGGTGTGGTGGTTTGATG+AGG 0.573076 6_4:+14663153 None:intergenic
GATATTGTGGCAACAATGAG+AGG 0.579136 6_4:+14662861 None:intergenic
GCTTCTTGCATCCATGGCAG+CGG 0.582295 6_4:-14663408 Msa0978630:CDS
TGAGACTGATACGAGGAAGA+GGG 0.588168 6_4:+14663030 None:intergenic
GGGAAGCAACACTTTCACTA+GGG 0.593182 6_4:-14662973 Msa0978630:CDS
CTCTGGGTGAGAGGATATTG+TGG 0.607413 6_4:+14662848 None:intergenic
GCCATGTTGAACAAATTGAA+CGG 0.631679 6_4:+14663303 None:intergenic
AACATGTAGTCACTATTGAA+GGG 0.632684 6_4:+14662924 None:intergenic
GAGACTGATACGAGGAAGAG+GGG 0.635701 6_4:+14663031 None:intergenic
AAGTGTTGCTTCCCAAATGG+AGG 0.651772 6_4:+14662982 None:intergenic
ATATTGTGGCAACAATGAGA+GGG 0.653605 6_4:+14662862 None:intergenic
GTTGTGATATCAGATTGAGA+AGG 0.660118 6_4:+14663357 None:intergenic
AGAGTTAGCCAAAACACGCG+TGG 0.681164 6_4:-14663089 Msa0978630:CDS
GGGAATCACAGAAAAGTGGG+TGG 0.688066 6_4:+14663051 None:intergenic
GAGCCGTTACTGTCAAAATG+CGG 0.711062 6_4:-14662828 Msa0978630:CDS
TCGAGCATGAGACTGATACG+AGG 0.743456 6_4:+14663023 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! GGTAAAATGTAATAATGATT+TGG + chr6_4:14662958-14662977 None:intergenic 20.0%
! GTAATAATGATTTGGAACAG+AGG + chr6_4:14662950-14662969 None:intergenic 30.0%
TGAATGGTAATTTGAAGACT+GGG + chr6_4:14662990-14663009 None:intergenic 30.0%
ATGAATGGTAATTTGAAGAC+TGG + chr6_4:14662991-14663010 None:intergenic 30.0%
! GATGAGGTAGATATTTTGTT+TGG + chr6_4:14663055-14663074 None:intergenic 30.0%
!! TTTGTTGTTGTTCTTGTTGT+TGG + chr6_4:14663089-14663108 None:intergenic 30.0%
AAAATTATCTCTCCTCCATT+TGG - chr6_4:14663227-14663246 Msa0978630:CDS 30.0%
AAATTATCTCTCCTCCATTT+GGG - chr6_4:14663228-14663247 Msa0978630:CDS 30.0%
AACATGTAGTCACTATTGAA+GGG + chr6_4:14663300-14663319 None:intergenic 30.0%
GTTGTGATATCAGATTGAGA+AGG + chr6_4:14662867-14662886 None:intergenic 35.0%
! TCCGTTCAATTTGTTCAACA+TGG - chr6_4:14662917-14662936 Msa0978630:CDS 35.0%
GCCATGTTGAACAAATTGAA+CGG + chr6_4:14662921-14662940 None:intergenic 35.0%
!! GGTAGATATTTTGTTTGGAG+AGG + chr6_4:14663050-14663069 None:intergenic 35.0%
!! ACTATTGAAGGGTTGATGTT+GGG + chr6_4:14663289-14663308 None:intergenic 35.0%
GAACATGTAGTCACTATTGA+AGG + chr6_4:14663301-14663320 None:intergenic 35.0%
ATATTGTGGCAACAATGAGA+GGG + chr6_4:14663362-14663381 None:intergenic 35.0%
CAAAATGCGGCAATGAAAAA+TGG - chr6_4:14663406-14663425 Msa0978630:CDS 35.0%
TCAGATTGAGAAGGTCTGTT+GGG + chr6_4:14662858-14662877 None:intergenic 40.0%
ATCAGATTGAGAAGGTCTGT+TGG + chr6_4:14662859-14662878 None:intergenic 40.0%
TTGAAGACTGGGAACTTGAA+GGG + chr6_4:14662979-14662998 None:intergenic 40.0%
TTTGAAGACTGGGAACTTGA+AGG + chr6_4:14662980-14662999 None:intergenic 40.0%
! TCGTTTTGCTCAGAGATGAA+TGG + chr6_4:14663006-14663025 None:intergenic 40.0%
!! TGTTGTTCTTGTTGTTGGTG+TGG + chr6_4:14663084-14663103 None:intergenic 40.0%
GGCTAACTCTTATCAACCAA+GGG + chr6_4:14663122-14663141 None:intergenic 40.0%
TGGCTAACTCTTATCAACCA+AGG + chr6_4:14663123-14663142 None:intergenic 40.0%
!! TGAAAGTGTTGCTTCCCAAA+TGG + chr6_4:14663245-14663264 None:intergenic 40.0%
!! CACTATTGAAGGGTTGATGT+TGG + chr6_4:14663290-14663309 None:intergenic 40.0%
TGACTACATGTTCCCTGAAA+AGG - chr6_4:14663308-14663327 Msa0978630:CDS 40.0%
!!! CAATGAGAGGGTTTTTTCCA+TGG + chr6_4:14663350-14663369 None:intergenic 40.0%
GATATTGTGGCAACAATGAG+AGG + chr6_4:14663363-14663382 None:intergenic 40.0%
!! ATTTTGACAGTAACGGCTCT+GGG + chr6_4:14663392-14663411 None:intergenic 40.0%
!! TTGCCGCATTTTGACAGTAA+CGG + chr6_4:14663399-14663418 None:intergenic 40.0%
ATGCGGCAATGAAAAATGGA+AGG - chr6_4:14663410-14663429 Msa0978630:CDS 40.0%
TGTTTGGAGAGGTGACAGAA+TGG + chr6_4:14663039-14663058 None:intergenic 45.0%
!! TGTTCTTGTTGTTGGTGTGG+TGG + chr6_4:14663081-14663100 None:intergenic 45.0%
TATCAACCAAGGGCGAAGTA+GGG + chr6_4:14663112-14663131 None:intergenic 45.0%
TTATCAACCAAGGGCGAAGT+AGG + chr6_4:14663113-14663132 None:intergenic 45.0%
GAGGGGAATCACAGAAAAGT+GGG + chr6_4:14663176-14663195 None:intergenic 45.0%
AGAGGGGAATCACAGAAAAG+TGG + chr6_4:14663177-14663196 None:intergenic 45.0%
TGAGACTGATACGAGGAAGA+GGG + chr6_4:14663194-14663213 None:intergenic 45.0%
ATGAGACTGATACGAGGAAG+AGG + chr6_4:14663195-14663214 None:intergenic 45.0%
!! AAGTGTTGCTTCCCAAATGG+AGG + chr6_4:14663242-14663261 None:intergenic 45.0%
TGGGAAGCAACACTTTCACT+AGG - chr6_4:14663247-14663266 Msa0978630:intron 45.0%
GGGAAGCAACACTTTCACTA+GGG - chr6_4:14663248-14663267 Msa0978630:intron 45.0%
!! GAAGGGTTGATGTTGGGAAT+AGG + chr6_4:14663283-14663302 None:intergenic 45.0%
! TGACAGCAACGACCTTTTCA+GGG + chr6_4:14663323-14663342 None:intergenic 45.0%
!! CATTTTGACAGTAACGGCTC+TGG + chr6_4:14663393-14663412 None:intergenic 45.0%
GAGCCGTTACTGTCAAAATG+CGG - chr6_4:14663393-14663412 Msa0978630:CDS 45.0%
TGGAGAGGTGACAGAATGGA+GGG + chr6_4:14663035-14663054 None:intergenic 50.0%
TTGGAGAGGTGACAGAATGG+AGG + chr6_4:14663036-14663055 None:intergenic 50.0%
GTTGGTGTGGTGGTTTGATG+AGG + chr6_4:14663071-14663090 None:intergenic 50.0%
AACAAACCCTACTTCGCCCT+TGG - chr6_4:14663103-14663122 Msa0978630:intron 50.0%
AGAGTTAGCCAAAACACGCG+TGG - chr6_4:14663132-14663151 Msa0978630:CDS 50.0%
! GAGTTTTGCCACGCGTGTTT+TGG + chr6_4:14663143-14663162 None:intergenic 50.0%
GGGAATCACAGAAAAGTGGG+TGG + chr6_4:14663173-14663192 None:intergenic 50.0%
GAGACTGATACGAGGAAGAG+GGG + chr6_4:14663193-14663212 None:intergenic 50.0%
TCGAGCATGAGACTGATACG+AGG + chr6_4:14663201-14663220 None:intergenic 50.0%
! GTGACAGCAACGACCTTTTC+AGG + chr6_4:14663324-14663343 None:intergenic 50.0%
CTCTGGGTGAGAGGATATTG+TGG + chr6_4:14663376-14663395 None:intergenic 50.0%
GCTTCTTGCATCCATGGCAG+CGG - chr6_4:14662813-14662832 Msa0978630:CDS 55.0%
GTCGTTGCTGTCACGTGCCA+TGG - chr6_4:14663330-14663349 Msa0978630:CDS 60.0%
!! CAGTAACGGCTCTGGGTGAG+AGG + chr6_4:14663385-14663404 None:intergenic 60.0%
CCAGTCGACAGCCGCTGCCA+TGG + chr6_4:14662827-14662846 None:intergenic 70.0%
CCATGGCAGCGGCTGTCGAC+TGG - chr6_4:14662824-14662843 Msa0978630:CDS 70.0%
Chromosome Type Strat End Strand Name
chr6_4 gene 14662808 14663435 14662808 ID=Msa0978630;Name=Msa0978630
chr6_4 mRNA 14662808 14663435 14662808 ID=Msa0978630-mRNA-1;Parent=Msa0978630;Name=Msa0978630-mRNA-1;_AED=0.48;_eAED=0.88;_QI=0|0|0|1|0|0|3|0|192
chr6_4 exon 14663292 14663435 14663292 ID=Msa0978630-mRNA-1:exon:4813;Parent=Msa0978630-mRNA-1
chr6_4 exon 14663119 14663251 14663119 ID=Msa0978630-mRNA-1:exon:4812;Parent=Msa0978630-mRNA-1
chr6_4 exon 14662808 14663109 14662808 ID=Msa0978630-mRNA-1:exon:4811;Parent=Msa0978630-mRNA-1
chr6_4 CDS 14663292 14663435 14663292 ID=Msa0978630-mRNA-1:cds;Parent=Msa0978630-mRNA-1
chr6_4 CDS 14663119 14663251 14663119 ID=Msa0978630-mRNA-1:cds;Parent=Msa0978630-mRNA-1
chr6_4 CDS 14662808 14663109 14662808 ID=Msa0978630-mRNA-1:cds;Parent=Msa0978630-mRNA-1
Gene Sequence

>Msa0978630

ATTTTGCTTCTTGCATCCATGGCAGCGGCTGTCGACTGGTCTAAACTCCCAACAGACCTTCTCAATCTGATATCACAACGAATCGACGATGAACTTGATCTCATTCGCTTCCGTTCAATTTGTTCAACATGGCGCTCTTCCTCTTCTTCAAATTACCATTCATCTCTGAGCAAAACGACAATAACCCTCCATTCTGTCACCTCTCCAAACAAAATATCTACCTCATCAAACCACCACACCAACAACAAGAACAACAACAAACCCTACTTCGCCCTTGAGTTAGCCAAAACACGCGTGGCAAAACTCGATTCTTCCACCCACTTTTCTGTGATTCCCCTCTTCCTCGTATCAGTCTCATGCTCGATTTCAGAAAATTATCTCTCCTCCATTTGGGAAGCAACACTTTCACTAGGGACTACGACACCTATTCCCAACATCAACCCTTCAATAGTGACTACATGTTCCCTGAAAAGGTCGTTGCTGTCACGTGCCATGGAAAAAACCCTCTCATTGTTGCCACAATATCCTCTCACCCAGAGCCGTTACTGTCAAAATGCGGCAATGAAAAATGGAAGGTGA
Protein sequence

>Msa0978630

ILLLASMAAAVDWSKLPTDLLNLISQRIDDELDLIRFRSICSTWRSSSSSNYHSSLSKTTITLHSVTSPNKISTSSNHHTNNKNNNKPYFALELAKTRVAKLDSSTHFSVIPLFLVSVSCSISENYLSSIWEATLSLGTTTPIPNINPSIVTTCSLKRSLLSRAMEKTLSLLPQYPLTQSRYCQNAAMKNGR*