AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0531830

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0531830 MtrunA17_Chr4g0005201 70.345 145 7 2 1 111 652 794 7.55e-48 162
Msa0531830 MtrunA17_Chr5g0437741 51.034 145 35 2 1 111 644 786 3.03e-37 132
Msa0531830 MtrunA17_Chr5g0432851 48.387 93 42 3 8 96 509 599 1.54e-19 82.4
Msa0531830 MtrunA17_Chr5g0437731 68.519 54 17 0 1 54 76 129 3.16e-18 74.3
Msa0531830 MtrunA17_Chr3g0108301 48.193 83 38 2 17 96 518 598 4.00e-18 78.2
Msa0531830 MtrunA17_Chr4g0062911 48.193 83 38 2 17 96 509 589 1.19e-17 77.0
Msa0531830 MtrunA17_Chr8g0393211 43.820 89 44 3 17 101 537 623 1.22e-17 77.0
Msa0531830 MtrunA17_Chr6g0478621 45.783 83 40 2 17 96 540 620 2.94e-17 75.9
Msa0531830 MtrunA17_Chr7g0245171 45.783 83 40 2 17 96 498 578 9.25e-17 74.3
Msa0531830 MtrunA17_Chr1g0209521 44.565 92 41 2 11 94 518 607 1.59e-16 73.9
Msa0531830 MtrunA17_Chr5g0434551 43.373 83 42 2 17 96 502 582 1.83e-16 73.6
Msa0531830 MtrunA17_Chr3g0126281 45.977 87 42 2 13 96 215 299 3.90e-16 72.4
Msa0531830 MtrunA17_Chr3g0128551 55.556 63 25 1 17 76 506 568 7.95e-16 71.6
Msa0531830 MtrunA17_Chr5g0396941 45.783 83 40 2 17 96 464 544 1.33e-15 71.2
Msa0531830 MtrunA17_Chr8g0387791 44.578 83 41 2 17 96 487 567 3.88e-15 69.7
Msa0531830 MtrunA17_Chr3g0126271 45.783 83 40 2 17 96 485 565 4.51e-15 69.7
Msa0531830 MtrunA17_Chr5g0423121 45.238 84 40 3 15 94 496 577 1.02e-14 68.6
Msa0531830 MtrunA17_Chr1g0159161 46.914 81 40 2 17 96 450 528 1.17e-14 68.6
Msa0531830 MtrunA17_Chr5g0428541 43.678 87 43 3 15 96 474 559 8.98e-14 65.9
Msa0531830 MtrunA17_Chr7g0265601 39.362 94 41 2 17 96 540 631 1.81e-13 65.1
Msa0531830 MtrunA17_Chr7g0237801 45.882 85 39 2 1 80 533 615 1.98e-13 65.1
Msa0531830 MtrunA17_Chr8g0379571 43.939 66 32 2 16 76 543 608 1.37e-11 59.7
Msa0531830 MtrunA17_Chr1g0147701 45.312 64 30 2 18 76 505 568 1.55e-11 59.7
Msa0531830 MtrunA17_Chr3g0140861 51.852 54 26 0 4 57 816 869 2.64e-11 58.9
Msa0531830 MtrunA17_Chr8g0376301 55.319 47 21 0 30 76 287 333 9.03e-11 57.4
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0531830 AT3G51740.1 52.000 125 26 1 1 91 686 810 4.95e-33 121
Msa0531830 AT2G26730.1 49.398 83 37 2 17 96 511 591 4.29e-18 78.6
Msa0531830 AT5G58300.3 45.556 90 44 2 10 96 514 601 5.41e-18 78.2
Msa0531830 AT5G58300.1 45.556 90 44 2 10 96 514 601 5.41e-18 78.2
Msa0531830 AT5G58300.2 45.556 90 44 2 10 96 514 601 5.41e-18 78.2
Msa0531830 AT1G68400.1 50.575 87 36 2 13 94 522 606 7.05e-18 78.2
Msa0531830 AT3G08680.1 48.235 85 40 2 15 96 503 586 2.06e-17 76.6
Msa0531830 AT3G08680.2 48.235 85 40 2 15 96 503 586 2.06e-17 76.6
Msa0531830 AT5G05160.1 41.758 91 45 2 12 96 500 588 5.56e-17 75.5
Msa0531830 AT5G41680.2 45.455 88 43 2 12 96 214 299 1.46e-16 73.6
Msa0531830 AT5G41680.1 45.455 88 43 2 12 96 240 325 1.65e-16 73.6
Msa0531830 AT1G64210.1 41.379 87 43 2 17 96 468 553 1.65e-15 71.2
Msa0531830 AT1G48480.1 40.449 89 48 2 17 100 533 621 1.90e-15 71.2
Msa0531830 AT4G23740.1 44.578 83 41 2 17 96 500 580 2.61e-15 70.9
Msa0531830 AT4G23740.2 44.578 83 41 2 17 96 500 580 2.61e-15 70.9
Msa0531830 AT3G17840.1 52.381 63 27 1 17 76 527 589 4.20e-15 70.1
Msa0531830 AT3G24660.1 42.424 99 49 3 1 95 525 619 4.98e-14 67.0
Msa0531830 AT2G36570.1 43.878 98 31 3 17 94 522 615 2.16e-13 65.1
Msa0531830 AT5G53320.1 41.463 82 41 3 15 96 467 541 2.01e-12 62.4
Msa0531830 AT1G17230.2 42.308 78 40 2 4 80 954 1027 5.92e-12 61.2
Msa0531830 AT1G17230.1 42.308 78 40 2 4 80 954 1027 9.42e-12 60.5
Msa0531830 AT5G16590.1 42.857 70 35 2 17 81 504 573 1.13e-11 60.5
Msa0531830 AT3G02880.1 41.429 70 36 2 17 81 506 575 3.56e-11 58.9
Msa0531830 AT1G70110.1 44.186 86 37 5 13 95 506 583 6.04e-11 58.2
Msa0531830 AT3G49670.1 53.448 58 26 1 11 67 852 909 6.67e-11 58.2

Find 21 sgRNAs with CRISPR-Local

Find 36 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ACTTCAACTTCAACCAATTC+TGG 0.231695 4_1:+5955408 None:intergenic
TAGCCTCGGTGTTATCCTTT+TGG 0.257199 4_1:-5955673 Msa0531830:CDS
AAAGGAGATTAAACCAGAAT+TGG 0.330276 4_1:-5955421 Msa0531830:CDS
GCTATAAACGTCGGTCTTTG+TGG 0.378184 4_1:+5955692 None:intergenic
AGGTTGAAACAAATGAATAA+AGG 0.390932 4_1:-5955362 None:intergenic
TGCAAAACTTGTTTAACTTC+AGG 0.401562 4_1:+5955450 None:intergenic
ACTATTGATGCAACATATTG+AGG 0.434119 4_1:+5955600 None:intergenic
TTCTTTGTCTTTGAAAGCTC+CGG 0.445593 4_1:+5955720 None:intergenic
CATCAATAGTTAAAGAAGAA+TGG 0.451806 4_1:-5955587 Msa0531830:CDS
ATTGCTACAGCAGGAAGTCT+TGG 0.477792 4_1:-5955753 Msa0531830:CDS
GAAGTTGAAGTTGATGATGA+TGG 0.502154 4_1:-5955390 Msa0531830:CDS
TAAACGTCGGTCTTTGTGGT+AGG 0.507728 4_1:+5955696 None:intergenic
TCCTGCTGTAGCAATGATGT+TGG 0.533607 4_1:+5955761 None:intergenic
ACCAACATCATTGCTACAGC+AGG 0.542435 4_1:-5955762 Msa0531830:CDS
TACCAGTTAAGATCTCCAAA+AGG 0.566616 4_1:+5955658 None:intergenic
AAGACCGACGTTTATAGCCT+CGG 0.601601 4_1:-5955687 Msa0531830:CDS
TGTAGCAATGATGTTGGTGT+CGG 0.607361 4_1:+5955767 None:intergenic
AAGTCTTGGATACAATGCAC+CGG 0.639160 4_1:-5955739 Msa0531830:CDS
AGTTGATGATGATGGAGCAA+AGG 0.643329 4_1:-5955382 Msa0531830:CDS
AACACCGAGGCTATAAACGT+CGG 0.732258 4_1:+5955683 None:intergenic
TCTCCAAAAGGATAACACCG+AGG 0.782521 4_1:+5955670 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! CATCAATAGTTAAAGAAGAA+TGG - chr4_1:5955558-5955577 Msa0531830:intron 25.0%
ACTATTGATGCAACATATTG+AGG + chr4_1:5955548-5955567 None:intergenic 30.0%
! GACAAATGAAGTGTTTGATT+TGG - chr4_1:5955580-5955599 Msa0531830:CDS 30.0%
ATTAAGAAGTTCATCTCCTA+TGG + chr4_1:5955627-5955646 None:intergenic 30.0%
! TGCAAAACTTGTTTAACTTC+AGG + chr4_1:5955698-5955717 None:intergenic 30.0%
! ACAAGTTTTGCAGCAATTAA+AGG - chr4_1:5955706-5955725 Msa0531830:CDS 30.0%
AAAGGAGATTAAACCAGAAT+TGG - chr4_1:5955724-5955743 Msa0531830:CDS 30.0%
! TTCTTTGTCTTTGAAAGCTC+CGG + chr4_1:5955428-5955447 None:intergenic 35.0%
!! ATCCTTTTGGAGATCTTAAC+TGG - chr4_1:5955485-5955504 Msa0531830:intron 35.0%
TACCAGTTAAGATCTCCAAA+AGG + chr4_1:5955490-5955509 None:intergenic 35.0%
!!! ATGCCATTTTTTGATTCTCG+TGG + chr4_1:5955518-5955537 None:intergenic 35.0%
ACGAGAATCAAAAAATGGCA+TGG - chr4_1:5955517-5955536 Msa0531830:intron 35.0%
!! TGTTTGATTTGGAACTCATG+AGG - chr4_1:5955591-5955610 Msa0531830:CDS 35.0%
!! GTTTGATTTGGAACTCATGA+GGG - chr4_1:5955592-5955611 Msa0531830:CDS 35.0%
ACTTCAACTTCAACCAATTC+TGG + chr4_1:5955740-5955759 None:intergenic 35.0%
!! GAAGTTGAAGTTGATGATGA+TGG - chr4_1:5955755-5955774 Msa0531830:CDS 35.0%
TGTAGCAATGATGTTGGTGT+CGG + chr4_1:5955381-5955400 None:intergenic 40.0%
AAGTCTTGGATACAATGCAC+CGG - chr4_1:5955406-5955425 Msa0531830:CDS 40.0%
!!! CCATTTTTTGATTCTCGTGG+TGG + chr4_1:5955515-5955534 None:intergenic 40.0%
CCACCACGAGAATCAAAAAA+TGG - chr4_1:5955512-5955531 Msa0531830:intron 40.0%
AGAAGTTCATCTCCTATGGT+TGG + chr4_1:5955623-5955642 None:intergenic 40.0%
!! AGTTGATGATGATGGAGCAA+AGG - chr4_1:5955763-5955782 Msa0531830:CDS 40.0%
ACCAACATCATTGCTACAGC+AGG - chr4_1:5955383-5955402 Msa0531830:CDS 45.0%
TCCTGCTGTAGCAATGATGT+TGG + chr4_1:5955387-5955406 None:intergenic 45.0%
ATTGCTACAGCAGGAAGTCT+TGG - chr4_1:5955392-5955411 Msa0531830:CDS 45.0%
TAAACGTCGGTCTTTGTGGT+AGG + chr4_1:5955452-5955471 None:intergenic 45.0%
GCTATAAACGTCGGTCTTTG+TGG + chr4_1:5955456-5955475 None:intergenic 45.0%
AAGACCGACGTTTATAGCCT+CGG - chr4_1:5955458-5955477 Msa0531830:intron 45.0%
AACACCGAGGCTATAAACGT+CGG + chr4_1:5955465-5955484 None:intergenic 45.0%
!!! TAGCCTCGGTGTTATCCTTT+TGG - chr4_1:5955472-5955491 Msa0531830:intron 45.0%
TCTCCAAAAGGATAACACCG+AGG + chr4_1:5955478-5955497 None:intergenic 45.0%
! GATTTGGAACTCATGAGGGA+TGG - chr4_1:5955596-5955615 Msa0531830:CDS 45.0%
TTGATCCATCACCTTCTGCT+AGG - chr4_1:5955672-5955691 Msa0531830:CDS 45.0%
TTAACTTCAGGCCTAGCAGA+AGG + chr4_1:5955686-5955705 None:intergenic 45.0%
ATGAGGGATGGACCAACCAT+AGG - chr4_1:5955608-5955627 Msa0531830:CDS 50.0%
TCAGGCCTAGCAGAAGGTGA+TGG + chr4_1:5955680-5955699 None:intergenic 55.0%
Chromosome Type Strat End Strand Name
chr4_1 gene 5955365 5955802 5955365 ID=Msa0531830;Name=Msa0531830
chr4_1 mRNA 5955365 5955802 5955365 ID=Msa0531830-mRNA-1;Parent=Msa0531830;Name=Msa0531830-mRNA-1;_AED=0.40;_eAED=0.40;_QI=0|0|0|1|1|1|2|0|111
chr4_1 exon 5955576 5955802 5955576 ID=Msa0531830-mRNA-1:exon:2015;Parent=Msa0531830-mRNA-1
chr4_1 exon 5955365 5955473 5955365 ID=Msa0531830-mRNA-1:exon:2014;Parent=Msa0531830-mRNA-1
chr4_1 CDS 5955576 5955802 5955576 ID=Msa0531830-mRNA-1:cds;Parent=Msa0531830-mRNA-1
chr4_1 CDS 5955365 5955473 5955365 ID=Msa0531830-mRNA-1:cds;Parent=Msa0531830-mRNA-1
Gene Sequence

>Msa0531830

ATGACAACTTCAGCCGACACCAACATCATTGCTACAGCAGGAAGTCTTGGATACAATGCACCGGAGCTTTCAAAGACAAAGAAACCTACCACAAAGACCGACGTTTATAGCCTCGGTGTTATCCTTTTGGAGATCTTAACTGGTAAACCACCACGAGAATCAAAAAATGGCATGGACTTGCCTCAATATGTTGCATCAATAGTTAAAGAAGAATGGACAAATGAAGTGCCTGAAGTTAAACAAGTTTTGCAGCAATTAAAGGAGATTAAACCAGAATTGGTTGAAGTTGAAGTTGAAGTTGATGATGATGGAGCAAAGGTTGAAACAAATGAATAA
Protein sequence

>Msa0531830

MTTSADTNIIATAGSLGYNAPELSKTKKPTTKTDVYSLGVILLEILTGKPPRESKNGMDLPQYVASIVKEEWTNEVPEVKQVLQQLKEIKPELVEVEVEVDDDGAKVETNE*