AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0666710

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0666710 MtrunA17_Chr4g0005201 98.925 93 1 0 1 93 652 744 1.09e-57 189
Msa0666710 MtrunA17_Chr5g0437741 77.419 93 21 0 1 93 644 736 1.02e-43 150
Msa0666710 MtrunA17_Chr4g0062911 60.000 70 25 1 17 83 509 578 3.30e-22 89.4
Msa0666710 MtrunA17_Chr5g0432851 55.000 80 32 2 8 83 509 588 5.52e-22 89.0
Msa0666710 MtrunA17_Chr5g0396941 53.659 82 34 2 17 95 464 544 6.06e-21 85.9
Msa0666710 MtrunA17_Chr8g0387791 52.439 82 35 2 17 95 487 567 6.33e-21 85.9
Msa0666710 MtrunA17_Chr6g0478621 58.571 70 26 1 17 83 540 609 7.88e-21 85.5
Msa0666710 MtrunA17_Chr8g0393211 57.143 70 27 1 17 83 537 606 8.50e-21 85.5
Msa0666710 MtrunA17_Chr5g0434551 54.286 70 29 1 17 83 502 571 8.88e-21 85.5
Msa0666710 MtrunA17_Chr7g0245171 55.714 70 28 1 17 83 498 567 8.94e-21 85.5
Msa0666710 MtrunA17_Chr3g0108301 55.714 70 28 1 17 83 518 587 1.54e-20 84.7
Msa0666710 MtrunA17_Chr1g0209521 54.321 81 29 2 11 83 518 598 1.71e-20 84.7
Msa0666710 MtrunA17_Chr3g0126281 55.405 74 30 1 13 83 215 288 1.72e-20 83.6
Msa0666710 MtrunA17_Chr5g0428541 48.810 84 38 2 17 95 476 559 3.04e-20 84.0
Msa0666710 MtrunA17_Chr5g0437731 74.074 54 14 0 1 54 76 129 3.69e-20 79.0
Msa0666710 MtrunA17_Chr3g0128551 51.220 82 36 2 17 95 506 586 4.05e-20 83.6
Msa0666710 MtrunA17_Chr5g0423121 52.055 73 31 2 15 83 496 568 1.26e-18 79.3
Msa0666710 MtrunA17_Chr1g0159161 51.220 82 34 3 17 95 450 528 3.43e-18 78.2
Msa0666710 MtrunA17_Chr3g0126271 52.857 70 30 1 17 83 485 554 4.31e-18 77.8
Msa0666710 MtrunA17_Chr7g0237801 45.455 88 41 2 1 83 533 618 3.74e-16 72.0
Msa0666710 MtrunA17_Chr7g0265601 41.975 81 33 1 17 83 540 620 5.13e-15 68.9
Msa0666710 MtrunA17_Chr1g0147701 41.758 91 44 3 18 100 505 594 1.00e-14 68.2
Msa0666710 MtrunA17_Chr5g0445251 47.561 82 37 2 15 96 88 163 2.94e-14 65.5
Msa0666710 MtrunA17_Chr2g0292521 44.444 90 44 2 1 84 937 1026 4.10e-14 66.2
Msa0666710 MtrunA17_Chr5g0440581 34.579 107 59 3 1 96 863 969 1.09e-13 65.1
Msa0666710 MtrunA17_Chr6g0478181 44.737 76 30 3 20 85 437 510 1.16e-13 65.1
Msa0666710 MtrunA17_Chr8g0379571 46.377 69 30 2 16 78 543 610 3.97e-13 63.5
Msa0666710 MtrunA17_Chr2g0288391 56.604 53 21 1 32 84 517 567 4.60e-13 63.5
Msa0666710 MtrunA17_Chr6g0488771 40.659 91 46 2 18 100 297 387 5.70e-13 63.2
Msa0666710 MtrunA17_Chr2g0279071 43.590 78 36 2 10 81 289 364 7.42e-13 62.8
Msa0666710 MtrunA17_Chr1g0169841 43.617 94 48 3 11 99 973 1066 7.92e-13 62.8
Msa0666710 MtrunA17_Chr2g0312651 46.575 73 37 2 11 81 971 1043 2.08e-12 61.6
Msa0666710 MtrunA17_Chr8g0376301 54.717 53 24 0 32 84 289 341 3.86e-12 60.8
Msa0666710 MtrunA17_Chr2g0280191 41.758 91 49 3 13 100 855 944 4.54e-12 60.5
Msa0666710 MtrunA17_Chr2g0313911 45.205 73 37 1 12 81 234 306 5.27e-12 60.1
Msa0666710 MtrunA17_Chr2g0324931 45.714 70 37 1 13 81 858 927 5.97e-12 60.1
Msa0666710 MtrunA17_Chr8g0388991 37.778 90 49 3 18 100 507 596 9.33e-12 59.7
Msa0666710 MtrunA17_Chr5g0442151 41.414 99 43 6 11 100 845 937 9.51e-12 59.7
Msa0666710 MtrunA17_Chr5g0400681 58.182 55 22 1 11 64 854 908 1.09e-11 59.7
Msa0666710 MtrunA17_Chr7g0261331 50.943 53 26 0 1 53 1082 1134 1.56e-11 58.9
Msa0666710 MtrunA17_Chr4g0060011 42.029 69 37 1 13 78 477 545 1.88e-11 58.9
Msa0666710 MtrunA17_Chr3g0129391 39.796 98 54 3 1 94 1025 1121 2.13e-11 58.5
Msa0666710 MtrunA17_Chr4g0046511 42.857 70 39 1 13 81 861 930 4.02e-11 57.8
Msa0666710 MtrunA17_Chr3g0117921 48.276 58 28 1 30 87 541 596 5.50e-11 57.4
Msa0666710 MtrunA17_Chr4g0054521 53.448 58 26 1 11 67 851 908 6.74e-11 57.4
Msa0666710 MtrunA17_Chr2g0277081 46.667 75 37 2 11 82 849 923 7.36e-11 57.0
Msa0666710 MtrunA17_Chr8g0373501 43.023 86 41 3 1 85 485 563 8.89e-11 57.0
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0666710 AT3G51740.1 76.344 93 22 0 1 93 686 778 3.83e-44 152
Msa0666710 AT3G08680.1 50.000 84 39 1 15 95 503 586 1.12e-22 91.3
Msa0666710 AT3G08680.2 50.000 84 39 1 15 95 503 586 1.12e-22 91.3
Msa0666710 AT1G68400.1 57.895 76 27 1 13 83 522 597 7.87e-22 89.0
Msa0666710 AT2G26730.1 60.000 70 25 1 17 83 511 580 3.12e-21 87.0
Msa0666710 AT5G41680.2 54.054 74 31 1 12 82 214 287 2.83e-20 83.2
Msa0666710 AT5G41680.1 54.054 74 31 1 12 82 240 313 4.71e-20 83.2
Msa0666710 AT5G58300.3 53.247 77 33 1 10 83 514 590 4.94e-20 83.6
Msa0666710 AT5G58300.1 53.247 77 33 1 10 83 514 590 4.94e-20 83.6
Msa0666710 AT5G58300.2 53.247 77 33 1 10 83 514 590 4.94e-20 83.6
Msa0666710 AT3G17840.1 55.072 69 28 1 17 82 527 595 9.75e-20 82.8
Msa0666710 AT5G05160.1 46.154 78 36 1 12 83 500 577 5.95e-19 80.5
Msa0666710 AT4G23740.1 54.286 70 29 1 17 83 500 569 7.02e-19 80.5
Msa0666710 AT4G23740.2 54.286 70 29 1 17 83 500 569 7.02e-19 80.5
Msa0666710 AT1G64210.1 44.186 86 41 2 17 95 468 553 1.31e-18 79.7
Msa0666710 AT1G48480.1 50.725 69 31 1 17 82 533 601 5.16e-18 77.8
Msa0666710 AT2G36570.1 45.263 95 32 3 7 83 514 606 1.45e-16 73.9
Msa0666710 AT3G24660.1 47.126 87 42 2 1 83 525 611 2.05e-16 73.2
Msa0666710 AT5G16590.1 48.571 70 33 1 17 83 504 573 2.50e-15 70.1
Msa0666710 AT5G53320.1 46.377 69 32 1 15 83 467 530 3.47e-15 69.7
Msa0666710 AT3G02880.1 40.244 82 46 1 17 95 506 587 7.02e-15 68.9
Msa0666710 AT5G24100.1 38.272 81 48 2 16 95 504 583 5.10e-14 66.6
Msa0666710 AT1G17230.1 44.565 92 48 3 11 99 961 1052 1.53e-13 65.1
Msa0666710 AT5G63930.1 43.678 87 47 2 11 95 967 1053 2.37e-13 64.7
Msa0666710 AT5G63930.2 43.678 87 47 2 11 95 903 989 2.43e-13 64.7
Msa0666710 AT1G17230.2 42.424 99 54 3 4 99 954 1052 2.94e-13 64.3
Msa0666710 AT4G20940.1 44.048 84 41 2 1 78 907 990 1.04e-12 62.8
Msa0666710 AT3G49670.1 50.000 74 34 2 11 81 852 925 1.15e-12 62.8
Msa0666710 AT1G08590.1 39.583 96 55 2 1 93 878 973 1.20e-12 62.8
Msa0666710 AT2G33170.2 47.143 70 35 2 11 78 987 1056 5.50e-12 60.8
Msa0666710 AT2G33170.1 47.143 70 35 2 11 78 987 1056 5.50e-12 60.8
Msa0666710 AT5G20690.1 35.106 94 55 2 11 98 542 635 6.80e-12 60.5
Msa0666710 AT1G34420.1 36.559 93 56 2 3 94 847 937 1.72e-11 59.3
Msa0666710 AT5G65700.1 55.172 58 25 1 11 67 856 913 2.04e-11 59.3
Msa0666710 AT5G65700.2 55.172 58 25 1 11 67 856 913 2.04e-11 59.3
Msa0666710 AT4G31250.1 36.471 85 48 3 16 95 529 612 2.61e-11 58.9
Msa0666710 AT5G62710.1 40.845 71 39 1 11 78 473 543 3.11e-11 58.5
Msa0666710 AT4G39400.1 45.238 84 43 2 13 94 1047 1129 3.44e-11 58.5
Msa0666710 AT5G62710.2 40.845 71 39 1 11 78 439 509 3.48e-11 58.5
Msa0666710 AT1G78530.1 44.444 72 37 1 13 81 234 305 4.30e-11 58.2
Msa0666710 AT5G07620.1 33.981 103 64 2 1 99 229 331 6.64e-11 57.4
Msa0666710 AT3G24240.1 41.860 86 45 2 12 95 956 1038 8.01e-11 57.4

Find 26 sgRNAs with CRISPR-Local

Find 28 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CAGCCTCGGTGTTATCCTTT+TGG 0.248528 4_4:+6833809 Msa0666710:CDS
GTCAAATGAAGTGTTTGATT+TGG 0.324262 4_4:+6833917 Msa0666710:CDS
TTCTTTGTCTTTGAAAGCTC+TGG 0.341174 4_4:-6833762 None:intergenic
ATGCCATTTGTTGGTTCTCC+TGG 0.362960 4_4:-6833852 None:intergenic
TTTAAGAAGTTCATCTCCTA+TGG 0.410729 4_4:-6833961 None:intergenic
GGCAAGTCCATGCCATTTGT+TGG 0.425256 4_4:-6833861 None:intergenic
CATCCATTGTTAAAGAAGAA+TGG 0.441053 4_4:+6833895 Msa0666710:CDS
ACAATGGATGCAACATATTG+AGG 0.461356 4_4:-6833882 None:intergenic
ATTGCTACAGCAGGAAGTCT+TGG 0.477792 4_4:+6833729 Msa0666710:CDS
TGACCATTCTTCTTTAACAA+TGG 0.478093 4_4:-6833898 None:intergenic
AGAAGTTCATCTCCTATGGT+TGG 0.529629 4_4:-6833957 None:intergenic
TCCTGCTGTAGCAATGATGT+TGG 0.533607 4_4:-6833721 None:intergenic
GATTTGGAACTCATGAGGGA+TGG 0.537502 4_4:+6833933 Msa0666710:CDS
CCACCAGGAGAACCAACAAA+TGG 0.539629 4_4:+6833849 Msa0666710:CDS
ACCAACATCATTGCTACAGC+AGG 0.542435 4_4:+6833720 Msa0666710:CDS
CCATTTGTTGGTTCTCCTGG+TGG 0.548920 4_4:-6833849 None:intergenic
TACCAGTTAAGAGTTCCAAA+AGG 0.550195 4_4:-6833824 None:intergenic
TGTAGCAATGATGTTGGTGT+TGG 0.550967 4_4:-6833715 None:intergenic
CTCTTAACTGGTAAACCACC+AGG 0.563734 4_4:+6833834 Msa0666710:CDS
TGTTTGATTTGGAACTCATG+AGG 0.576156 4_4:+6833928 Msa0666710:CDS
AAAACCGACGTTTACAGCCT+CGG 0.583782 4_4:+6833795 Msa0666710:CDS
AGGAGAACCAACAAATGGCA+TGG 0.605960 4_4:+6833854 Msa0666710:CDS
ATGAGGGATGGACCAACCAT+AGG 0.609052 4_4:+6833945 Msa0666710:CDS
GTTTGATTTGGAACTCATGA+GGG 0.628775 4_4:+6833929 Msa0666710:CDS
AACACCGAGGCTGTAAACGT+CGG 0.738905 4_4:-6833799 None:intergenic
GTTCCAAAAGGATAACACCG+AGG 0.781912 4_4:-6833812 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
CATCCATTGTTAAAGAAGAA+TGG + chr4_4:6833895-6833914 Msa0666710:CDS 30.0%
TGACCATTCTTCTTTAACAA+TGG - chr4_4:6833901-6833920 None:intergenic 30.0%
! GTCAAATGAAGTGTTTGATT+TGG + chr4_4:6833917-6833936 Msa0666710:CDS 30.0%
TTTAAGAAGTTCATCTCCTA+TGG - chr4_4:6833964-6833983 None:intergenic 30.0%
! TTCTTTGTCTTTGAAAGCTC+TGG - chr4_4:6833765-6833784 None:intergenic 35.0%
!!! ATCCTTTTGGAACTCTTAAC+TGG + chr4_4:6833822-6833841 Msa0666710:CDS 35.0%
TACCAGTTAAGAGTTCCAAA+AGG - chr4_4:6833827-6833846 None:intergenic 35.0%
ACAATGGATGCAACATATTG+AGG - chr4_4:6833885-6833904 None:intergenic 35.0%
!! TGTTTGATTTGGAACTCATG+AGG + chr4_4:6833928-6833947 Msa0666710:CDS 35.0%
!! GTTTGATTTGGAACTCATGA+GGG + chr4_4:6833929-6833948 Msa0666710:CDS 35.0%
TGTAGCAATGATGTTGGTGT+TGG - chr4_4:6833718-6833737 None:intergenic 40.0%
!!! TAAACGTCGGTTTTTGTCGT+AGG - chr4_4:6833789-6833808 None:intergenic 40.0%
AGAAGTTCATCTCCTATGGT+TGG - chr4_4:6833960-6833979 None:intergenic 40.0%
ACCAACATCATTGCTACAGC+AGG + chr4_4:6833720-6833739 Msa0666710:CDS 45.0%
TCCTGCTGTAGCAATGATGT+TGG - chr4_4:6833724-6833743 None:intergenic 45.0%
ATTGCTACAGCAGGAAGTCT+TGG + chr4_4:6833729-6833748 Msa0666710:CDS 45.0%
AAAACCGACGTTTACAGCCT+CGG + chr4_4:6833795-6833814 Msa0666710:CDS 45.0%
GTTCCAAAAGGATAACACCG+AGG - chr4_4:6833815-6833834 None:intergenic 45.0%
CTCTTAACTGGTAAACCACC+AGG + chr4_4:6833834-6833853 Msa0666710:CDS 45.0%
!! ATGCCATTTGTTGGTTCTCC+TGG - chr4_4:6833855-6833874 None:intergenic 45.0%
AGGAGAACCAACAAATGGCA+TGG + chr4_4:6833854-6833873 Msa0666710:CDS 45.0%
! GATTTGGAACTCATGAGGGA+TGG + chr4_4:6833933-6833952 Msa0666710:CDS 45.0%
AACACCGAGGCTGTAAACGT+CGG - chr4_4:6833802-6833821 None:intergenic 50.0%
!!! CAGCCTCGGTGTTATCCTTT+TGG + chr4_4:6833809-6833828 Msa0666710:CDS 50.0%
!! CCATTTGTTGGTTCTCCTGG+TGG - chr4_4:6833852-6833871 None:intergenic 50.0%
CCACCAGGAGAACCAACAAA+TGG + chr4_4:6833849-6833868 Msa0666710:CDS 50.0%
! GGCAAGTCCATGCCATTTGT+TGG - chr4_4:6833864-6833883 None:intergenic 50.0%
ATGAGGGATGGACCAACCAT+AGG + chr4_4:6833945-6833964 Msa0666710:CDS 50.0%
Chromosome Type Strat End Strand Name
chr4_4 gene 6833702 6834004 6833702 ID=Msa0666710;Name=Msa0666710
chr4_4 mRNA 6833702 6834004 6833702 ID=Msa0666710-mRNA-1;Parent=Msa0666710;Name=Msa0666710-mRNA-1;_AED=0.49;_eAED=0.49;_QI=0|-1|0|1|-1|1|1|0|100
chr4_4 exon 6833702 6834004 6833702 ID=Msa0666710-mRNA-1:exon:2227;Parent=Msa0666710-mRNA-1
chr4_4 CDS 6833702 6834004 6833702 ID=Msa0666710-mRNA-1:cds;Parent=Msa0666710-mRNA-1
Gene Sequence

>Msa0666710

ATGACAACTTCAGCCAACACCAACATCATTGCTACAGCAGGAAGTCTTGGATACAATGCACCAGAGCTTTCAAAGACAAAGAAACCTACGACAAAAACCGACGTTTACAGCCTCGGTGTTATCCTTTTGGAACTCTTAACTGGTAAACCACCAGGAGAACCAACAAATGGCATGGACTTGCCTCAATATGTTGCATCCATTGTTAAAGAAGAATGGTCAAATGAAGTGTTTGATTTGGAACTCATGAGGGATGGACCAACCATAGGAGATGAACTTCTTAAAATTAGCTTTGCATTGTGTTGA
Protein sequence

>Msa0666710

MTTSANTNIIATAGSLGYNAPELSKTKKPTTKTDVYSLGVILLELLTGKPPGEPTNGMDLPQYVASIVKEEWSNEVFDLELMRDGPTIGDELLKISFALC*