AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene88105

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene88105.t1 MTR_1g007990 75.926 54 13 0 41 94 912 965 3.57e-22 89.7
MS.gene88105.t1 MTR_8g036130 80.000 45 9 0 4 48 3 47 1.85e-17 74.7
MS.gene88105.t1 MTR_4g032620 75.000 48 11 1 1 48 1 47 3.39e-17 73.9
MS.gene88105.t1 MTR_1g090697 41.593 113 45 5 4 99 3 111 5.59e-16 68.9
MS.gene88105.t1 MTR_1g090783 54.839 62 24 1 4 65 2 59 5.71e-16 68.9
MS.gene88105.t1 MTR_5g047580 40.179 112 48 2 4 100 3 110 6.09e-16 68.9
MS.gene88105.t1 MTR_1g077390 36.937 111 51 3 4 99 3 109 1.26e-14 65.5
MS.gene88105.t1 MTR_3g466830 68.889 45 14 0 4 48 2 46 1.82e-14 65.5
MS.gene88105.t1 MTR_4g028800 74.419 43 9 1 6 48 5 45 2.09e-14 62.8
MS.gene88105.t1 MTR_2g016210 72.093 43 12 0 6 48 5 47 2.61e-14 66.2
MS.gene88105.t1 MTR_3g466890 44.444 90 45 2 4 93 2 86 5.76e-14 63.9
MS.gene88105.t1 MTR_3g466980 64.444 45 16 0 4 48 3 47 1.37e-13 63.9
MS.gene88105.t1 MTR_4g031910 48.598 107 44 3 4 104 3 104 2.62e-13 63.5
MS.gene88105.t1 MTR_3g031240 33.945 109 60 4 1 103 1 103 3.78e-13 62.4
MS.gene88105.t1 MTR_3g065100 44.037 109 49 3 4 100 3 111 1.51e-12 61.6
MS.gene88105.t1 MTR_4g063790 54.348 46 21 0 4 49 3 48 3.60e-12 59.7
MS.gene88105.t1 MTR_5g075380 62.791 43 16 0 6 48 5 47 3.83e-12 59.3
MS.gene88105.t1 MTR_2g035610 80.000 45 9 0 4 48 3 47 4.17e-12 58.2
MS.gene88105.t1 MTR_1g090710 48.438 64 28 2 1 64 1 59 4.76e-12 58.9
MS.gene88105.t1 MTR_4g028720 47.191 89 41 2 4 92 3 85 5.15e-12 58.9
MS.gene88105.t1 MTR_4g019670 36.036 111 59 3 3 105 5 111 1.62e-11 59.3
MS.gene88105.t1 MTR_7g106510 34.234 111 61 3 3 105 5 111 2.68e-11 58.9
MS.gene88105.t1 MTR_7g011950 47.191 89 41 2 4 92 3 85 6.07e-11 56.2
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene88105.t1 AT3G05860 43.182 88 45 2 4 91 3 85 1.76e-15 68.9
MS.gene88105.t1 AT3G05860 43.182 88 45 2 4 91 3 85 2.74e-15 68.9
MS.gene88105.t1 AT3G05860 43.182 88 45 2 4 91 3 85 3.36e-15 68.9
MS.gene88105.t1 AT1G22590 42.308 78 37 3 1 75 1 73 3.06e-12 59.7
MS.gene88105.t1 AT5G26580 35.000 100 60 3 1 99 1 96 5.06e-12 60.8
MS.gene88105.t1 AT1G31630 34.653 101 54 4 4 96 2 98 2.94e-11 58.5
MS.gene88105.t1 AT1G65330 55.556 45 20 0 4 48 2 46 5.65e-11 57.8
MS.gene88105.t1 AT5G26650 31.776 107 59 3 6 99 3 108 6.75e-11 57.8

Find 16 sgRNAs with CRISPR-Local

Find 24 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TCATTGTCAATGATGCTTCT+AGG 0.238280 4.2:+73432386 MS.gene88105:CDS
TTCAACATTTCCGTAGCTTC+TGG 0.330276 4.2:-73432654 None:intergenic
TTACTACTGAAGATTGAAAA+AGG 0.333620 4.2:+73432699 MS.gene88105:CDS
GAAGAAGAGTCTATTCAAAA+AGG 0.366702 4.2:+73432429 MS.gene88105:CDS
GGAAAGCAACATACAAGAAA+AGG 0.449202 4.2:+73432407 MS.gene88105:CDS
AACCTTACTTCTTCTACCCA+TGG 0.464315 4.2:-73432353 None:intergenic
AACCATGGGTAGAAGAAGTA+AGG 0.501192 4.2:+73432351 None:intergenic
AGAAGCATCATTGACAATGA+AGG 0.508760 4.2:-73432383 None:intergenic
TAGCACCCTATGTGGTATTG+AGG 0.514801 4.2:+73432462 MS.gene88105:CDS
ACAAGCCTCAATACCACATA+GGG 0.561401 4.2:-73432467 None:intergenic
GGATATTCCTCCAGAAGCTA+CGG 0.564585 4.2:+73432644 MS.gene88105:CDS
AACATTTCCGTAGCTTCTGG+AGG 0.585851 4.2:-73432651 None:intergenic
CCACAAGGAAAATATATGCA+AGG 0.593677 4.2:-73432612 None:intergenic
GTTGAACTTAGCACCCTATG+TGG 0.618465 4.2:+73432454 MS.gene88105:CDS
CACAAGCCTCAATACCACAT+AGG 0.619824 4.2:-73432468 None:intergenic
ATATCCATCTTGTTCCCACA+AGG 0.643932 4.2:-73432627 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TTCATATTTGTATTATGTAT+AGG + chr4.2:73432544-73432563 MS.gene88105:intron 15.0%
!! TAAAAAACAGAATAGTTAGA+TGG - chr4.2:73432587-73432606 None:intergenic 20.0%
!!! ATCTAACTATTCTGTTTTTT+AGG + chr4.2:73432586-73432605 MS.gene88105:intron 20.0%
! TTACTACTGAAGATTGAAAA+AGG + chr4.2:73432699-73432718 MS.gene88105:CDS 25.0%
!! GTATTATGTATAGGTTTTTG+AGG + chr4.2:73432553-73432572 MS.gene88105:intron 25.0%
GAAGAAGAGTCTATTCAAAA+AGG + chr4.2:73432429-73432448 MS.gene88105:CDS 30.0%
! CTTGCATATATTTTCCTTGT+GGG + chr4.2:73432613-73432632 MS.gene88105:CDS 30.0%
CCACAAGGAAAATATATGCA+AGG - chr4.2:73432615-73432634 None:intergenic 35.0%
GGAAAGCAACATACAAGAAA+AGG + chr4.2:73432407-73432426 MS.gene88105:CDS 35.0%
TCATTGTCAATGATGCTTCT+AGG + chr4.2:73432386-73432405 MS.gene88105:CDS 35.0%
! CCTTGCATATATTTTCCTTG+TGG + chr4.2:73432612-73432631 MS.gene88105:CDS 35.0%
!! AGAAGCATCATTGACAATGA+AGG - chr4.2:73432386-73432405 None:intergenic 35.0%
ACAAGCCTCAATACCACATA+GGG - chr4.2:73432470-73432489 None:intergenic 40.0%
ATATCCATCTTGTTCCCACA+AGG - chr4.2:73432630-73432649 None:intergenic 40.0%
GAAATGCAGAACTCTCGTAA+AGG - chr4.2:73432507-73432526 None:intergenic 40.0%
TTCAACATTTCCGTAGCTTC+TGG - chr4.2:73432657-73432676 None:intergenic 40.0%
! TTTTCCTTGTGGGAACAAGA+TGG + chr4.2:73432623-73432642 MS.gene88105:CDS 40.0%
AACATTTCCGTAGCTTCTGG+AGG - chr4.2:73432654-73432673 None:intergenic 45.0%
CACAAGCCTCAATACCACAT+AGG - chr4.2:73432471-73432490 None:intergenic 45.0%
CTCGTAAAGGCCATACACTA+TGG - chr4.2:73432494-73432513 None:intergenic 45.0%
GGATATTCCTCCAGAAGCTA+CGG + chr4.2:73432644-73432663 MS.gene88105:CDS 45.0%
GTTGAACTTAGCACCCTATG+TGG + chr4.2:73432454-73432473 MS.gene88105:CDS 45.0%
TAGCACCCTATGTGGTATTG+AGG + chr4.2:73432462-73432481 MS.gene88105:CDS 45.0%
GAGGCTTGTGCCATAGTGTA+TGG + chr4.2:73432481-73432500 MS.gene88105:intron 50.0%


Chromosome Type Strat End Strand Name
chr4.2 gene 73432355 73432782 73432355 ID=MS.gene88105
chr4.2 mRNA 73432355 73432782 73432355 ID=MS.gene88105.t1;Parent=MS.gene88105
chr4.2 exon 73432355 73432497 73432355 ID=MS.gene88105.t1.exon1;Parent=MS.gene88105.t1
chr4.2 CDS 73432355 73432497 73432355 ID=cds.MS.gene88105.t1;Parent=MS.gene88105.t1
chr4.2 exon 73432608 73432782 73432608 ID=MS.gene88105.t1.exon2;Parent=MS.gene88105.t1
chr4.2 CDS 73432608 73432782 73432608 ID=cds.MS.gene88105.t1;Parent=MS.gene88105.t1
Gene Sequence

>MS.gene88105

ATGGGTAGAAGAAGTAAGGTTAAACATGCCTTCATTGTCAATGATGCTTCTAGGAAAGCAACATACAAGAAAAGGAAGAAGAGTCTATTCAAAAAGGTTGTTGAACTTAGCACCCTATGTGGTATTGAGGCTTGTGCCATAGTGTATGGCCTTTACGAGAGTTCTGCATTTCTTTGATTATGTTTTATATTCATATTTGTATTATGTATAGGTTTTTGAGGATAAACATCCATCTAACTATTCTGTTTTTTAGGAATCCTTGCATATATTTTCCTTGTGGGAACAAGATGGATATTCCTCCAGAAGCTACGGAAATGTTGAATCAGATTGAAGAAAAGAAAACATTACTACTGAAGATTGAAAAAGGTAGAAAAAAAGTTACTAAACATCTGAAGAAGTCTCAAGAAAAGTTCAAGAAAAAGAGTTGA
Protein sequence

>MS.gene88105.t1

MGRRSKVKHAFIVNDASRKATYKKRKKSLFKKVVELSTLCGIEACAIVNPCIYFPCGNKMDIPPEATEMLNQIEEKKTLLLKIEKGRKKVTKHLKKSQEKFKKKS