AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0746280

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0746280 MtrunA17_Chr6g0457521 50.365 137 50 5 1 130 49 174 1.48e-25 97.1
Msa0746280 MtrunA17_Chr6g0460421 56.250 80 27 2 9 86 2 75 9.05e-20 85.5
Msa0746280 MtrunA17_Chr6g0457551 85.366 41 6 0 9 49 2 42 1.93e-19 77.8
Msa0746280 MtrunA17_Chr1g0146381 66.667 51 17 0 6 56 2 52 2.84e-19 78.2
Msa0746280 MtrunA17_Chr6g0457541 85.106 47 6 1 11 56 4 50 2.62e-18 81.3
Msa0746280 MtrunA17_Chr6g0460451 57.692 78 29 2 9 86 2 75 5.63e-18 80.5
Msa0746280 MtrunA17_Chr3g0088921 74.510 51 13 0 7 57 1 51 6.53e-18 80.5
Msa0746280 MtrunA17_Chr6g0457531 57.971 69 29 0 9 77 2 70 8.61e-18 80.1
Msa0746280 MtrunA17_Chr3g0088671 77.778 45 10 0 9 53 2 46 2.46e-17 78.6
Msa0746280 MtrunA17_Chr3g0088571 70.833 48 14 0 9 56 2 49 3.41e-17 75.1
Msa0746280 MtrunA17_Chr3g0088741 59.155 71 25 2 9 75 2 72 4.68e-17 77.8
Msa0746280 MtrunA17_Chr3g0088601 50.000 86 42 1 6 91 11 95 8.30e-17 77.4
Msa0746280 MtrunA17_Chr2g0303111 74.468 47 12 0 7 53 1 47 9.02e-17 77.0
Msa0746280 MtrunA17_Chr3g0088651 75.000 44 11 0 9 52 2 45 9.05e-17 74.3
Msa0746280 MtrunA17_Chr3g0088691 75.000 44 11 0 9 52 2 45 1.23e-16 73.9
Msa0746280 MtrunA17_Chr6g0457501 70.833 48 14 0 9 56 2 49 4.59e-16 75.5
Msa0746280 MtrunA17_Chr3g0088551 72.917 48 13 0 9 56 2 49 4.71e-16 75.1
Msa0746280 MtrunA17_Chr1g0157711 48.649 74 36 1 7 78 1 74 1.41e-15 73.6
Msa0746280 MtrunA17_Chr3g0088951 70.000 50 14 1 9 57 2 51 2.68e-15 72.8
Msa0746280 MtrunA17_Chr3g0088721 62.000 50 19 0 4 53 1 50 2.82e-15 72.8
Msa0746280 MtrunA17_Chr3g0088591 47.436 78 33 1 6 83 15 84 3.25e-15 70.1
Msa0746280 MtrunA17_Chr3g0088631 56.452 62 27 0 9 70 2 63 6.53e-15 72.0
Msa0746280 MtrunA17_Chr3g0088621 46.753 77 33 1 8 84 12 80 2.31e-14 70.5
Msa0746280 MtrunA17_Chr3g0088991 55.224 67 19 2 7 62 1 67 4.47e-14 69.3
Msa0746280 MtrunA17_Chr3g0089001 55.385 65 18 2 9 62 32 96 1.59e-13 67.8
Msa0746280 MtrunA17_Chr3g0088841 66.667 48 15 1 7 53 1 48 2.00e-13 67.8
Msa0746280 MtrunA17_Chr3g0127321 65.306 49 16 1 6 53 28 76 3.02e-13 67.4
Msa0746280 MtrunA17_Chr3g0088701 56.667 60 25 1 4 63 1 59 3.09e-13 67.0
Msa0746280 MtrunA17_Chr1g0151721 53.425 73 23 2 5 67 14 85 3.26e-13 67.0
Msa0746280 MtrunA17_Chr3g0088751 64.583 48 16 1 9 56 2 48 3.91e-13 66.6
Msa0746280 MtrunA17_Chr3g0088661 56.667 60 25 1 4 63 1 59 6.00e-13 65.9
Msa0746280 MtrunA17_Chr3g0088931 64.583 48 16 1 11 57 4 51 9.36e-13 65.9
Msa0746280 MtrunA17_Chr1g0146401 49.296 71 32 1 11 77 21 91 2.91e-12 64.3
Msa0746280 MtrunA17_Chr3g0088541 66.667 42 14 0 10 51 2 43 6.23e-12 63.2
Msa0746280 MtrunA17_Chr3g0127311 59.574 47 19 0 7 53 2 48 7.18e-12 63.2
Msa0746280 MtrunA17_Chr3g0088831 40.000 85 39 2 3 87 7 79 1.39e-11 62.4
Msa0746280 MtrunA17_Chr1g0170781 68.293 41 13 0 5 45 12 52 1.47e-11 62.4
Msa0746280 MtrunA17_Chr7g0214521 62.000 50 17 2 8 55 8 57 2.27e-11 61.6
Msa0746280 MtrunA17_Chr3g0088531 50.847 59 28 1 12 70 3 60 4.22e-11 60.8
Msa0746280 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 5_1:+68433450 Msa0746280:CDS
TTTGTTGTTGTTCTTGTTGT+TGG 0.348750 5_1:-68433309 None:intergenic
AAATTATCTCTCCTCCATTT+GGG 0.404433 5_1:+68433451 Msa0746280:CDS
GAAGGGTTGATGTTGGGAAT+AGG 0.430716 5_1:-68433503 None:intergenic
TTATCAACCAAGGGCGAAGT+AGG 0.446707 5_1:-68433333 None:intergenic
ACTATTGAAGGGTTGATGTT+GGG 0.454182 5_1:-68433509 None:intergenic
AACAAACCCTACTTCGCCCT+TGG 0.463083 5_1:+68433326 Msa0746280:CDS
TGACTACATGTTCCCTGAAA+AGG 0.470098 5_1:+68433531 Msa0746280:CDS
GAACATGTAGTCACTATTGA+AGG 0.476485 5_1:-68433521 None:intergenic
GTCGTTGCTGTCACGTGCCA+TGG 0.491026 5_1:+68433553 Msa0746280:CDS
CACTATTGAAGGGTTGATGT+TGG 0.495406 5_1:-68433510 None:intergenic
TCAGATTGAGAAGGTCTGTT+GGG 0.508699 5_1:-68433078 None:intergenic
TGAAAGTGTTGCTTCCCAAA+TGG 0.510671 5_1:-68433465 None:intergenic
TGTTCTTGTTGTTGGTGTGG+TGG 0.515272 5_1:-68433301 None:intergenic
TGTTTGGAGAGGTGACAGAA+TGG 0.519350 5_1:-68433259 None:intergenic
TCCGTTCAATTTGTTCAACA+TGG 0.529209 5_1:+68433140 Msa0746280:CDS
CCAGTCGACAGCCGCTGCCA+TGG 0.531422 5_1:-68433047 None:intergenic
ATCAGATTGAGAAGGTCTGT+TGG 0.532634 5_1:-68433079 None:intergenic
TTGGAGAGGTGACAGAATGG+AGG 0.540854 5_1:-68433256 None:intergenic
TGGGAAGCAACACTTTCACT+AGG 0.545995 5_1:+68433470 Msa0746280:CDS
CAGTAACGGCTCTGGGTGAG+AGG 0.548246 5_1:-68433605 None:intergenic
TGTTGTTCTTGTTGTTGGTG+TGG 0.559442 5_1:-68433304 None:intergenic
GAGGGGAATCACAGAAAAGT+GGG 0.560445 5_1:-68433396 None:intergenic
TGGAGAGGTGACAGAATGGA+GGG 0.561195 5_1:-68433255 None:intergenic
ATGAGACTGATACGAGGAAG+AGG 0.565004 5_1:-68433415 None:intergenic
TATCAACCAAGGGCGAAGTA+GGG 0.568592 5_1:-68433332 None:intergenic
AGAGGGGAATCACAGAAAAG+TGG 0.571573 5_1:-68433397 None:intergenic
GTTGGTGTGGTGGTTTGATG+AGG 0.573076 5_1:-68433291 None:intergenic
GATATTGTGGCAACAATGAG+AGG 0.579136 5_1:-68433583 None:intergenic
GCTTCTTGCATCCATGGCAG+CGG 0.582295 5_1:+68433036 Msa0746280:CDS
TGAGACTGATACGAGGAAGA+GGG 0.588168 5_1:-68433414 None:intergenic
GGGAAGCAACACTTTCACTA+GGG 0.593182 5_1:+68433471 Msa0746280:CDS
CTCTGGGTGAGAGGATATTG+TGG 0.607413 5_1:-68433596 None:intergenic
GCCATGTTGAACAAATTGAA+CGG 0.631679 5_1:-68433141 None:intergenic
AACATGTAGTCACTATTGAA+GGG 0.632684 5_1:-68433520 None:intergenic
GAGACTGATACGAGGAAGAG+GGG 0.635701 5_1:-68433413 None:intergenic
AAGTGTTGCTTCCCAAATGG+AGG 0.651772 5_1:-68433462 None:intergenic
ATATTGTGGCAACAATGAGA+GGG 0.653605 5_1:-68433582 None:intergenic
GTTGTGATATCAGATTGAGA+AGG 0.660118 5_1:-68433087 None:intergenic
AGAGTTAGCCAAAACACGCG+TGG 0.681164 5_1:+68433355 Msa0746280:intron
GGGAATCACAGAAAAGTGGG+TGG 0.688066 5_1:-68433393 None:intergenic
GAGCCGTTACTGTCAAAATG+CGG 0.711062 5_1:+68433616 Msa0746280:CDS
TCGAGCATGAGACTGATACG+AGG 0.743456 5_1:-68433421 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! GGTAAAATGTAATAATGATT+TGG - chr5_1:68433181-68433200 None:intergenic 20.0%
! GTAATAATGATTTGGAACAG+AGG - chr5_1:68433173-68433192 None:intergenic 30.0%
TGAATGGTAATTTGAAGACT+GGG - chr5_1:68433213-68433232 None:intergenic 30.0%
ATGAATGGTAATTTGAAGAC+TGG - chr5_1:68433214-68433233 None:intergenic 30.0%
! GATGAGGTAGATATTTTGTT+TGG - chr5_1:68433278-68433297 None:intergenic 30.0%
!! TTTGTTGTTGTTCTTGTTGT+TGG - chr5_1:68433312-68433331 None:intergenic 30.0%
AAAATTATCTCTCCTCCATT+TGG + chr5_1:68433450-68433469 Msa0746280:CDS 30.0%
AAATTATCTCTCCTCCATTT+GGG + chr5_1:68433451-68433470 Msa0746280:CDS 30.0%
AACATGTAGTCACTATTGAA+GGG - chr5_1:68433523-68433542 None:intergenic 30.0%
GTTGTGATATCAGATTGAGA+AGG - chr5_1:68433090-68433109 None:intergenic 35.0%
! TCCGTTCAATTTGTTCAACA+TGG + chr5_1:68433140-68433159 Msa0746280:CDS 35.0%
GCCATGTTGAACAAATTGAA+CGG - chr5_1:68433144-68433163 None:intergenic 35.0%
!! GGTAGATATTTTGTTTGGAG+AGG - chr5_1:68433273-68433292 None:intergenic 35.0%
!! ACTATTGAAGGGTTGATGTT+GGG - chr5_1:68433512-68433531 None:intergenic 35.0%
GAACATGTAGTCACTATTGA+AGG - chr5_1:68433524-68433543 None:intergenic 35.0%
ATATTGTGGCAACAATGAGA+GGG - chr5_1:68433585-68433604 None:intergenic 35.0%
CAAAATGCGGCAATGAAAAA+TGG + chr5_1:68433629-68433648 Msa0746280:CDS 35.0%
TCAGATTGAGAAGGTCTGTT+GGG - chr5_1:68433081-68433100 None:intergenic 40.0%
ATCAGATTGAGAAGGTCTGT+TGG - chr5_1:68433082-68433101 None:intergenic 40.0%
TTGAAGACTGGGAACTTGAA+GGG - chr5_1:68433202-68433221 None:intergenic 40.0%
TTTGAAGACTGGGAACTTGA+AGG - chr5_1:68433203-68433222 None:intergenic 40.0%
! TCGTTTTGCTCAGAGATGAA+TGG - chr5_1:68433229-68433248 None:intergenic 40.0%
!! TGTTGTTCTTGTTGTTGGTG+TGG - chr5_1:68433307-68433326 None:intergenic 40.0%
GGCTAACTCTTATCAACCAA+GGG - chr5_1:68433345-68433364 None:intergenic 40.0%
TGGCTAACTCTTATCAACCA+AGG - chr5_1:68433346-68433365 None:intergenic 40.0%
!! TGAAAGTGTTGCTTCCCAAA+TGG - chr5_1:68433468-68433487 None:intergenic 40.0%
!! CACTATTGAAGGGTTGATGT+TGG - chr5_1:68433513-68433532 None:intergenic 40.0%
TGACTACATGTTCCCTGAAA+AGG + chr5_1:68433531-68433550 Msa0746280:CDS 40.0%
!!! CAATGAGAGGGTTTTTTCCA+TGG - chr5_1:68433573-68433592 None:intergenic 40.0%
GATATTGTGGCAACAATGAG+AGG - chr5_1:68433586-68433605 None:intergenic 40.0%
!! ATTTTGACAGTAACGGCTCT+GGG - chr5_1:68433615-68433634 None:intergenic 40.0%
!! TTGCCGCATTTTGACAGTAA+CGG - chr5_1:68433622-68433641 None:intergenic 40.0%
ATGCGGCAATGAAAAATGGA+AGG + chr5_1:68433633-68433652 Msa0746280:CDS 40.0%
TGTTTGGAGAGGTGACAGAA+TGG - chr5_1:68433262-68433281 None:intergenic 45.0%
!! TGTTCTTGTTGTTGGTGTGG+TGG - chr5_1:68433304-68433323 None:intergenic 45.0%
TATCAACCAAGGGCGAAGTA+GGG - chr5_1:68433335-68433354 None:intergenic 45.0%
TTATCAACCAAGGGCGAAGT+AGG - chr5_1:68433336-68433355 None:intergenic 45.0%
GAGGGGAATCACAGAAAAGT+GGG - chr5_1:68433399-68433418 None:intergenic 45.0%
AGAGGGGAATCACAGAAAAG+TGG - chr5_1:68433400-68433419 None:intergenic 45.0%
TGAGACTGATACGAGGAAGA+GGG - chr5_1:68433417-68433436 None:intergenic 45.0%
ATGAGACTGATACGAGGAAG+AGG - chr5_1:68433418-68433437 None:intergenic 45.0%
!! AAGTGTTGCTTCCCAAATGG+AGG - chr5_1:68433465-68433484 None:intergenic 45.0%
TGGGAAGCAACACTTTCACT+AGG + chr5_1:68433470-68433489 Msa0746280:CDS 45.0%
GGGAAGCAACACTTTCACTA+GGG + chr5_1:68433471-68433490 Msa0746280:CDS 45.0%
!! GAAGGGTTGATGTTGGGAAT+AGG - chr5_1:68433506-68433525 None:intergenic 45.0%
! TGACAGCAACGACCTTTTCA+GGG - chr5_1:68433546-68433565 None:intergenic 45.0%
!! CATTTTGACAGTAACGGCTC+TGG - chr5_1:68433616-68433635 None:intergenic 45.0%
GAGCCGTTACTGTCAAAATG+CGG + chr5_1:68433616-68433635 Msa0746280:CDS 45.0%
TGGAGAGGTGACAGAATGGA+GGG - chr5_1:68433258-68433277 None:intergenic 50.0%
TTGGAGAGGTGACAGAATGG+AGG - chr5_1:68433259-68433278 None:intergenic 50.0%
GTTGGTGTGGTGGTTTGATG+AGG - chr5_1:68433294-68433313 None:intergenic 50.0%
AACAAACCCTACTTCGCCCT+TGG + chr5_1:68433326-68433345 Msa0746280:CDS 50.0%
AGAGTTAGCCAAAACACGCG+TGG + chr5_1:68433355-68433374 Msa0746280:intron 50.0%
! GAGTTTTGCCACGCGTGTTT+TGG - chr5_1:68433366-68433385 None:intergenic 50.0%
GGGAATCACAGAAAAGTGGG+TGG - chr5_1:68433396-68433415 None:intergenic 50.0%
GAGACTGATACGAGGAAGAG+GGG - chr5_1:68433416-68433435 None:intergenic 50.0%
TCGAGCATGAGACTGATACG+AGG - chr5_1:68433424-68433443 None:intergenic 50.0%
! GTGACAGCAACGACCTTTTC+AGG - chr5_1:68433547-68433566 None:intergenic 50.0%
CTCTGGGTGAGAGGATATTG+TGG - chr5_1:68433599-68433618 None:intergenic 50.0%
GCTTCTTGCATCCATGGCAG+CGG + chr5_1:68433036-68433055 Msa0746280:CDS 55.0%
GTCGTTGCTGTCACGTGCCA+TGG + chr5_1:68433553-68433572 Msa0746280:CDS 60.0%
!! CAGTAACGGCTCTGGGTGAG+AGG - chr5_1:68433608-68433627 None:intergenic 60.0%
CCAGTCGACAGCCGCTGCCA+TGG - chr5_1:68433050-68433069 None:intergenic 70.0%
CCATGGCAGCGGCTGTCGAC+TGG + chr5_1:68433047-68433066 Msa0746280:CDS 70.0%
Chromosome Type Strat End Strand Name
chr5_1 gene 68433031 68433658 68433031 ID=Msa0746280;Name=Msa0746280
chr5_1 mRNA 68433031 68433658 68433031 ID=Msa0746280-mRNA-1;Parent=Msa0746280;Name=Msa0746280-mRNA-1;_AED=0.46;_eAED=0.87;_QI=0|0|0|1|0|0|3|0|192
chr5_1 exon 68433031 68433174 68433031 ID=Msa0746280-mRNA-1:exon:20433;Parent=Msa0746280-mRNA-1
chr5_1 exon 68433215 68433347 68433215 ID=Msa0746280-mRNA-1:exon:20434;Parent=Msa0746280-mRNA-1
chr5_1 exon 68433357 68433658 68433357 ID=Msa0746280-mRNA-1:exon:20435;Parent=Msa0746280-mRNA-1
chr5_1 CDS 68433031 68433174 68433031 ID=Msa0746280-mRNA-1:cds;Parent=Msa0746280-mRNA-1
chr5_1 CDS 68433215 68433347 68433215 ID=Msa0746280-mRNA-1:cds;Parent=Msa0746280-mRNA-1
chr5_1 CDS 68433357 68433658 68433357 ID=Msa0746280-mRNA-1:cds;Parent=Msa0746280-mRNA-1
Gene Sequence

>Msa0746280

ATTTTGCTTCTTGCATCCATGGCAGCGGCTGTCGACTGGTCTAAACTCCCAACAGACCTTCTCAATCTGATATCACAACGAATCGACGATGAACTTGATCTCATTCGCTTCCGTTCAATTTGTTCAACATGGCGCTCTTCCTCTTCTTCAAATTACCATTCATCTCTGAGCAAAACGACAATAACCCTCCATTCTGTCACCTCTCCAAACAAAATATCTACCTCATCAAACCACCACACCAACAACAAGAACAACAACAAACCCTACTTCGCCCTTGAGTTAGCCAAAACACGCGTGGCAAAACTCGATTCTTCCACCCACTTTTCTGTGATTCCCCTCTTCCTCGTATCAGTCTCATGCTCGATTTCAGAAAATTATCTCTCCTCCATTTGGGAAGCAACACTTTCACTAGGGACTACGACACCTATTCCCAACATCAACCCTTCAATAGTGACTACATGTTCCCTGAAAAGGTCGTTGCTGTCACGTGCCATGGAAAAAACCCTCTCATTGTTGCCACAATATCCTCTCACCCAGAGCCGTTACTGTCAAAATGCGGCAATGAAAAATGGAAGGTGA
Protein sequence

>Msa0746280

ILLLASMAAAVDWSKLPTDLLNLISQRIDDELDLIRFRSICSTWRSSSSSNYHSSLSKTTITLHSVTSPNKISTSSNHHTNNKNNNKPYFALELAKTRVAKLDSSTHFSVIPLFLVSVSCSISENYLSSIWEATLSLGTTTPIPNINPSIVTTCSLKRSLLSRAMEKTLSLLPQYPLTQSRYCQNAAMKNGR*