AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene27809

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene27809.t1 MTR_4g065087 97.581 124 3 0 1 124 300 423 1.20e-85 262
MS.gene27809.t1 MTR_8g086490 97.581 124 3 0 1 124 300 423 1.20e-85 262
MS.gene27809.t1 MTR_0722s0020 68.750 128 22 2 3 127 363 475 3.09e-56 183
MS.gene27809.t1 MTR_4g130920 57.391 115 46 3 11 124 499 611 7.89e-36 130
MS.gene27809.t1 MTR_1g100787 40.625 96 57 0 29 124 964 1059 4.66e-16 73.9
MS.gene27809.t1 MTR_3g009400 39.815 108 64 1 18 124 865 972 5.03e-14 68.2
MS.gene27809.t1 MTR_3g095100 39.623 106 63 1 20 124 836 941 1.98e-13 66.2
MS.gene27809.t1 MTR_8g088760 38.384 99 55 2 29 124 276 371 4.89e-13 65.1
MS.gene27809.t1 MTR_7g080810 32.710 107 71 1 17 123 262 367 3.44e-12 62.8
MS.gene27809.t1 MTR_4g091570 37.975 79 49 0 46 124 743 821 1.63e-11 60.8
MS.gene27809.t1 MTR_6g009370 33.333 99 65 1 24 122 270 367 3.70e-11 59.7
MS.gene27809.t1 MTR_7g062950 40.260 77 45 1 46 121 329 405 8.05e-11 58.9
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene27809.t1 AT5G45800 71.429 119 34 0 7 125 344 462 3.33e-59 190
MS.gene27809.t1 AT5G45800 72.034 118 33 0 7 124 344 461 5.57e-58 190
MS.gene27809.t1 AT2G24230 53.509 114 52 1 11 124 500 612 1.22e-36 132
MS.gene27809.t1 AT5G58150 39.167 120 70 1 4 123 470 586 3.56e-21 88.6
MS.gene27809.t1 AT5G07280 41.935 93 54 0 29 121 888 980 3.88e-18 79.7
MS.gene27809.t1 AT4G39400 40.741 108 63 1 18 124 842 949 1.01e-15 72.8
MS.gene27809.t1 AT1G55610 38.889 108 65 1 18 124 818 925 7.51e-14 67.8
MS.gene27809.t1 AT1G55610 38.889 108 65 1 18 124 818 925 7.51e-14 67.8
MS.gene27809.t1 AT3G13380 42.268 97 56 0 28 124 828 924 2.45e-13 66.2
MS.gene27809.t1 AT3G45410 40.260 77 46 0 45 121 329 405 4.68e-12 62.4
MS.gene27809.t1 AT2G01950 37.736 106 65 1 20 124 799 904 8.49e-12 61.6
MS.gene27809.t1 AT4G03230 35.000 80 52 0 45 124 520 599 2.01e-11 60.5
MS.gene27809.t1 AT4G03230 35.000 80 52 0 45 124 605 684 2.05e-11 60.5
MS.gene27809.t1 AT3G45330 36.735 98 53 2 26 121 321 411 2.12e-11 60.5
MS.gene27809.t1 AT4G03230 35.000 80 52 0 45 124 577 656 2.17e-11 60.5
MS.gene27809.t1 AT4G03230 35.000 80 52 0 45 124 577 656 2.17e-11 60.5
MS.gene27809.t1 AT4G03230 35.000 80 52 0 45 124 512 591 2.20e-11 60.5
MS.gene27809.t1 AT4G03230 35.000 80 52 0 45 124 677 756 2.41e-11 60.5
MS.gene27809.t1 AT4G03230 35.000 80 52 0 45 124 677 756 2.41e-11 60.5
MS.gene27809.t1 AT4G03230 35.000 80 52 0 45 124 519 598 2.44e-11 60.5
MS.gene27809.t1 AT3G45420 37.662 77 48 0 45 121 337 413 5.89e-11 59.3
MS.gene27809.t1 AT2G37710 38.961 77 46 1 46 121 335 411 9.57e-11 58.5

Find 29 sgRNAs with CRISPR-Local

Find 29 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CCAAACTTGTTGCCTCTTTC+TGG 0.082970 4.3:-14056413 MS.gene27809:CDS
CTTTCTGGTTACTGTATTGC+AGG 0.256729 4.3:-14056398 MS.gene27809:CDS
TAATTGCCACGTCACATTTC+GGG 0.263652 4.3:-14056592 MS.gene27809:CDS
ATAATTGCCACGTCACATTT+CGG 0.305057 4.3:-14056593 MS.gene27809:CDS
CCAGAAAGAGGCAACAAGTT+TGG 0.349422 4.3:+14056413 None:intergenic
TTTGAGTTTGAAACAGAATC+AGG 0.357790 4.3:-14056707 MS.gene27809:CDS
GATTCTGTTTCAAACTCAAA+TGG 0.432700 4.3:+14056710 None:intergenic
AAGGTGTGGACCAGTGTATT+GGG 0.438562 4.3:-14056546 MS.gene27809:CDS
GAAGGTGTGGACCAGTGTAT+TGG 0.439569 4.3:-14056547 MS.gene27809:CDS
GATTGCCACGTGTATTTCAC+CGG 0.454025 4.3:+14056514 None:intergenic
AACACAAAGGTTGAGAAAAC+AGG 0.460190 4.3:-14056734 MS.gene27809:CDS
TTGAATGTGAAGTTCATCAA+TGG 0.462646 4.3:+14056623 None:intergenic
TGAAATACACGTGGCAATCA+AGG 0.486909 4.3:-14056510 MS.gene27809:CDS
GTGTATTGGGCCGTGTTACC+CGG 0.528951 4.3:-14056533 MS.gene27809:CDS
ATCACCACTGCTGCAGATGT+TGG 0.537029 4.3:+14056656 None:intergenic
AAACAGAATCAGGTTCAACA+TGG 0.549823 4.3:-14056697 MS.gene27809:CDS
GCAATACAGTAACCAGAAAG+AGG 0.549855 4.3:+14056401 None:intergenic
GGTAACACGGCCCAATACAC+TGG 0.552985 4.3:+14056536 None:intergenic
GTGTATTTCACCGGGTAACA+CGG 0.553649 4.3:+14056523 None:intergenic
AAAGAGTCACAGCTAGCAGA+AGG 0.595614 4.3:-14056569 MS.gene27809:CDS
AGAACCAACATCTGCAGCAG+TGG 0.602503 4.3:-14056660 MS.gene27809:CDS
AGTCACAGCTAGCAGAAGGA+AGG 0.615444 4.3:-14056565 MS.gene27809:CDS
CAGCTAGCAGAAGGAAGGTG+TGG 0.620715 4.3:-14056560 MS.gene27809:CDS
ATTGCCACGTGTATTTCACC+GGG 0.626192 4.3:+14056515 None:intergenic
AACAGAATCAGGTTCAACAT+GGG 0.632520 4.3:-14056696 MS.gene27809:CDS
CTCTTTCCCGAAATGTGACG+TGG 0.635097 4.3:+14056586 None:intergenic
GATGAACACGACAAACACAA+AGG 0.686114 4.3:-14056747 MS.gene27809:CDS
TGTTGATTATGATGACTCTG+TGG 0.704964 4.3:-14056468 MS.gene27809:CDS
GTTACCCGGTGAAATACACG+TGG 0.737461 4.3:-14056519 MS.gene27809:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! ATTGAATCATTTTTTCTATA+CGG + chr4.3:14056742-14056761 None:intergenic 15.0%
GATTCTGTTTCAAACTCAAA+TGG + chr4.3:14056397-14056416 None:intergenic 30.0%
TTGAATGTGAAGTTCATCAA+TGG + chr4.3:14056484-14056503 None:intergenic 30.0%
! TTTGAGTTTGAAACAGAATC+AGG - chr4.3:14056397-14056416 MS.gene27809:CDS 30.0%
AAACAGAATCAGGTTCAACA+TGG - chr4.3:14056407-14056426 MS.gene27809:CDS 35.0%
AACACAAAGGTTGAGAAAAC+AGG - chr4.3:14056370-14056389 MS.gene27809:CDS 35.0%
AACAGAATCAGGTTCAACAT+GGG - chr4.3:14056408-14056427 MS.gene27809:CDS 35.0%
ATAATTGCCACGTCACATTT+CGG - chr4.3:14056511-14056530 MS.gene27809:CDS 35.0%
! TGTTGATTATGATGACTCTG+TGG - chr4.3:14056636-14056655 MS.gene27809:CDS 35.0%
GCAATACAGTAACCAGAAAG+AGG + chr4.3:14056706-14056725 None:intergenic 40.0%
TAATTGCCACGTCACATTTC+GGG - chr4.3:14056512-14056531 MS.gene27809:CDS 40.0%
TGAAATACACGTGGCAATCA+AGG - chr4.3:14056594-14056613 MS.gene27809:CDS 40.0%
!! CTTTCTGGTTACTGTATTGC+AGG - chr4.3:14056706-14056725 MS.gene27809:CDS 40.0%
AAAGAGTCACAGCTAGCAGA+AGG - chr4.3:14056535-14056554 MS.gene27809:CDS 45.0%
AAGGTGTGGACCAGTGTATT+GGG - chr4.3:14056558-14056577 MS.gene27809:CDS 45.0%
ATTGCCACGTGTATTTCACC+GGG + chr4.3:14056592-14056611 None:intergenic 45.0%
CCAGAAAGAGGCAACAAGTT+TGG + chr4.3:14056694-14056713 None:intergenic 45.0%
GATTGCCACGTGTATTTCAC+CGG + chr4.3:14056593-14056612 None:intergenic 45.0%
GTGTATTTCACCGGGTAACA+CGG + chr4.3:14056584-14056603 None:intergenic 45.0%
!! CCAAACTTGTTGCCTCTTTC+TGG - chr4.3:14056691-14056710 MS.gene27809:CDS 45.0%
AGAACCAACATCTGCAGCAG+TGG - chr4.3:14056444-14056463 MS.gene27809:CDS 50.0%
AGTCACAGCTAGCAGAAGGA+AGG - chr4.3:14056539-14056558 MS.gene27809:CDS 50.0%
ATCACCACTGCTGCAGATGT+TGG + chr4.3:14056451-14056470 None:intergenic 50.0%
CTCTTTCCCGAAATGTGACG+TGG + chr4.3:14056521-14056540 None:intergenic 50.0%
GTTACCCGGTGAAATACACG+TGG - chr4.3:14056585-14056604 MS.gene27809:CDS 50.0%
! GAAGGTGTGGACCAGTGTAT+TGG - chr4.3:14056557-14056576 MS.gene27809:CDS 50.0%
CAGCTAGCAGAAGGAAGGTG+TGG - chr4.3:14056544-14056563 MS.gene27809:CDS 55.0%
GGTAACACGGCCCAATACAC+TGG + chr4.3:14056571-14056590 None:intergenic 55.0%
GTGTATTGGGCCGTGTTACC+CGG - chr4.3:14056571-14056590 MS.gene27809:CDS 55.0%


Chromosome Type Strat End Strand Name
chr4.3 gene 14056358 14056768 14056358 ID=MS.gene27809
chr4.3 mRNA 14056358 14056768 14056358 ID=MS.gene27809.t1;Parent=MS.gene27809
chr4.3 exon 14056358 14056768 14056358 ID=MS.gene27809.t1.exon1;Parent=MS.gene27809.t1
chr4.3 CDS 14056358 14056768 14056358 ID=cds.MS.gene27809.t1;Parent=MS.gene27809.t1
Gene Sequence

>MS.gene27809

ATGAACACGACAAACACAAAGGTTGAGAAAACAGGACCATTTGAGTTTGAAACAGAATCAGGTTCAACATGGGTTGCAGATGTGAAAGAACCAACATCTGCAGCAGTGGTGATGTTTGAGAAACCATTGATGAACTTCACATTCAAAGATCTCATAATTGCCACGTCACATTTCGGGAAAGAGTCACAGCTAGCAGAAGGAAGGTGTGGACCAGTGTATTGGGCCGTGTTACCCGGTGAAATACACGTGGCAATCAAGGTTCTTGAACATGTCAGAGATGTTGATTATGATGACTCTGTGGCTATGTTTGTTGAATTATCGAAACTGAAACATCCAAACTTGTTGCCTCTTTCTGGTTACTGTATTGCAGGTATGTGTGTGCCGTATAGAAAAAATGATTCAATGTTTTGA
Protein sequence

>MS.gene27809.t1

MNTTNTKVEKTGPFEFETESGSTWVADVKEPTSAAVVMFEKPLMNFTFKDLIIATSHFGKESQLAEGRCGPVYWAVLPGEIHVAIKVLEHVRDVDYDDSVAMFVELSKLKHPNLLPLSGYCIAGMCVPYRKNDSMF