AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene000084

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene000084.t1 MTR_1g007990 75.926 54 13 0 41 94 912 965 3.57e-22 89.7
MS.gene000084.t1 MTR_8g036130 80.000 45 9 0 4 48 3 47 1.85e-17 74.7
MS.gene000084.t1 MTR_4g032620 75.000 48 11 1 1 48 1 47 3.39e-17 73.9
MS.gene000084.t1 MTR_1g090697 41.593 113 45 5 4 99 3 111 5.59e-16 68.9
MS.gene000084.t1 MTR_1g090783 54.839 62 24 1 4 65 2 59 5.71e-16 68.9
MS.gene000084.t1 MTR_5g047580 40.179 112 48 2 4 100 3 110 6.09e-16 68.9
MS.gene000084.t1 MTR_1g077390 36.937 111 51 3 4 99 3 109 1.26e-14 65.5
MS.gene000084.t1 MTR_3g466830 68.889 45 14 0 4 48 2 46 1.82e-14 65.5
MS.gene000084.t1 MTR_4g028800 74.419 43 9 1 6 48 5 45 2.09e-14 62.8
MS.gene000084.t1 MTR_2g016210 72.093 43 12 0 6 48 5 47 2.61e-14 66.2
MS.gene000084.t1 MTR_3g466890 44.444 90 45 2 4 93 2 86 5.76e-14 63.9
MS.gene000084.t1 MTR_3g466980 64.444 45 16 0 4 48 3 47 1.37e-13 63.9
MS.gene000084.t1 MTR_4g031910 48.598 107 44 3 4 104 3 104 2.62e-13 63.5
MS.gene000084.t1 MTR_3g031240 33.945 109 60 4 1 103 1 103 3.78e-13 62.4
MS.gene000084.t1 MTR_3g065100 44.037 109 49 3 4 100 3 111 1.51e-12 61.6
MS.gene000084.t1 MTR_4g063790 54.348 46 21 0 4 49 3 48 3.60e-12 59.7
MS.gene000084.t1 MTR_5g075380 62.791 43 16 0 6 48 5 47 3.83e-12 59.3
MS.gene000084.t1 MTR_2g035610 80.000 45 9 0 4 48 3 47 4.17e-12 58.2
MS.gene000084.t1 MTR_1g090710 48.438 64 28 2 1 64 1 59 4.76e-12 58.9
MS.gene000084.t1 MTR_4g028720 47.191 89 41 2 4 92 3 85 5.15e-12 58.9
MS.gene000084.t1 MTR_4g019670 36.036 111 59 3 3 105 5 111 1.62e-11 59.3
MS.gene000084.t1 MTR_7g106510 34.234 111 61 3 3 105 5 111 2.68e-11 58.9
MS.gene000084.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.gene000084.t1 AT3G05860 43.182 88 45 2 4 91 3 85 1.76e-15 68.9
MS.gene000084.t1 AT3G05860 43.182 88 45 2 4 91 3 85 2.74e-15 68.9
MS.gene000084.t1 AT3G05860 43.182 88 45 2 4 91 3 85 3.36e-15 68.9
MS.gene000084.t1 AT1G22590 42.308 78 37 3 1 75 1 73 3.06e-12 59.7
MS.gene000084.t1 AT5G26580 35.000 100 60 3 1 99 1 96 5.06e-12 60.8
MS.gene000084.t1 AT1G31630 34.653 101 54 4 4 96 2 98 2.94e-11 58.5
MS.gene000084.t1 AT1G65330 55.556 45 20 0 4 48 2 46 5.65e-11 57.8
MS.gene000084.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 4.4:-71825007 MS.gene000084:CDS
TTCAACATTTCCGTAGCTTC+TGG 0.330276 4.4:+71824739 None:intergenic
TTACTACTGAAGATTGAAAA+AGG 0.333620 4.4:-71824694 MS.gene000084:CDS
GAAGAAGAGTCTATTCAAAA+AGG 0.366702 4.4:-71824964 MS.gene000084:CDS
GGAAAGCAACATACAAGAAA+AGG 0.449202 4.4:-71824986 MS.gene000084:CDS
AACCTTACTTCTTCTACCCA+TGG 0.464315 4.4:+71825040 None:intergenic
AACCATGGGTAGAAGAAGTA+AGG 0.501192 4.4:-71825042 None:intergenic
AGAAGCATCATTGACAATGA+AGG 0.508760 4.4:+71825010 None:intergenic
TAGCACCCTATGTGGTATTG+AGG 0.514801 4.4:-71824931 MS.gene000084:CDS
ACAAGCCTCAATACCACATA+GGG 0.561401 4.4:+71824926 None:intergenic
GGATATTCCTCCAGAAGCTA+CGG 0.564585 4.4:-71824749 MS.gene000084:CDS
AACATTTCCGTAGCTTCTGG+AGG 0.585851 4.4:+71824742 None:intergenic
CCACAAGGAAAATATATGCA+AGG 0.593677 4.4:+71824781 None:intergenic
GTTGAACTTAGCACCCTATG+TGG 0.618465 4.4:-71824939 MS.gene000084:CDS
CACAAGCCTCAATACCACAT+AGG 0.619824 4.4:+71824925 None:intergenic
ATATCCATCTTGTTCCCACA+AGG 0.643932 4.4:+71824766 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TTCATATTTGTATTATGTAT+AGG - chr4.4:71824822-71824841 MS.gene000084:intron 15.0%
!! TAAAAAACAGAATAGTTAGA+TGG + chr4.4:71824865-71824884 None:intergenic 20.0%
!!! ATCTAACTATTCTGTTTTTT+AGG - chr4.4:71824864-71824883 MS.gene000084:intron 20.0%
! TTACTACTGAAGATTGAAAA+AGG - chr4.4:71824977-71824996 MS.gene000084:CDS 25.0%
!! GTATTATGTATAGGTTTTTG+AGG - chr4.4:71824831-71824850 MS.gene000084:intron 25.0%
GAAGAAGAGTCTATTCAAAA+AGG - chr4.4:71824707-71824726 MS.gene000084:CDS 30.0%
! CTTGCATATATTTTCCTTGT+GGG - chr4.4:71824891-71824910 MS.gene000084:intron 30.0%
CCACAAGGAAAATATATGCA+AGG + chr4.4:71824893-71824912 None:intergenic 35.0%
GGAAAGCAACATACAAGAAA+AGG - chr4.4:71824685-71824704 MS.gene000084:CDS 35.0%
TCATTGTCAATGATGCTTCT+AGG - chr4.4:71824664-71824683 MS.gene000084:CDS 35.0%
! CCTTGCATATATTTTCCTTG+TGG - chr4.4:71824890-71824909 MS.gene000084:intron 35.0%
!! AGAAGCATCATTGACAATGA+AGG + chr4.4:71824664-71824683 None:intergenic 35.0%
ACAAGCCTCAATACCACATA+GGG + chr4.4:71824748-71824767 None:intergenic 40.0%
ATATCCATCTTGTTCCCACA+AGG + chr4.4:71824908-71824927 None:intergenic 40.0%
GAAATGCAGAACTCTCGTAA+AGG + chr4.4:71824785-71824804 None:intergenic 40.0%
TTCAACATTTCCGTAGCTTC+TGG + chr4.4:71824935-71824954 None:intergenic 40.0%
! TTTTCCTTGTGGGAACAAGA+TGG - chr4.4:71824901-71824920 MS.gene000084:intron 40.0%
AACATTTCCGTAGCTTCTGG+AGG + chr4.4:71824932-71824951 None:intergenic 45.0%
CACAAGCCTCAATACCACAT+AGG + chr4.4:71824749-71824768 None:intergenic 45.0%
CTCGTAAAGGCCATACACTA+TGG + chr4.4:71824772-71824791 None:intergenic 45.0%
GGATATTCCTCCAGAAGCTA+CGG - chr4.4:71824922-71824941 MS.gene000084:CDS 45.0%
GTTGAACTTAGCACCCTATG+TGG - chr4.4:71824732-71824751 MS.gene000084:CDS 45.0%
TAGCACCCTATGTGGTATTG+AGG - chr4.4:71824740-71824759 MS.gene000084:CDS 45.0%
GAGGCTTGTGCCATAGTGTA+TGG - chr4.4:71824759-71824778 MS.gene000084:CDS 50.0%


Chromosome Type Strat End Strand Name
chr4.4 gene 71824633 71825060 71824633 ID=MS.gene000084
chr4.4 mRNA 71824633 71825060 71824633 ID=MS.gene000084.t1;Parent=MS.gene000084
chr4.4 exon 71824918 71825060 71824918 ID=MS.gene000084.t1.exon1;Parent=MS.gene000084.t1
chr4.4 CDS 71824918 71825060 71824918 ID=cds.MS.gene000084.t1;Parent=MS.gene000084.t1
chr4.4 exon 71824633 71824807 71824633 ID=MS.gene000084.t1.exon2;Parent=MS.gene000084.t1
chr4.4 CDS 71824633 71824807 71824633 ID=cds.MS.gene000084.t1;Parent=MS.gene000084.t1
Gene Sequence

>MS.gene000084

ATGGGTAGAAGAAGTAAGGTTAAACATGCCTTCATTGTCAATGATGCTTCTAGGAAAGCAACATACAAGAAAAGGAAGAAGAGTCTATTCAAAAAGGTTGTTGAACTTAGCACCCTATGTGGTATTGAGGCTTGTGCCATAGTGTATGGCCTTTACGAGAGTTCTGCATTTCTTTGATTATGTTTTATATTCATATTTGTATTATGTATAGGTTTTTGAGGATAAACATCCATCTAACTATTCTGTTTTTTAGGAATCCTTGCATATATTTTCCTTGTGGGAACAAGATGGATATTCCTCCAGAAGCTACGGAAATGTTGAATCAGATTGAAGAAAAGAAAACATTACTACTGAAGATTGAAAAAGGTAGAAAAAAAGTTACTAAACATCTGAAGAAGTCTCAAGAAAAGTTCAAGAAAAAGAGTTGA
Protein sequence

>MS.gene000084.t1

MGRRSKVKHAFIVNDASRKATYKKRKKSLFKKVVELSTLCGIEACAIVNPCIYFPCGNKMDIPPEATEMLNQIEEKKTLLLKIEKGRKKVTKHLKKSQEKFKKKS