AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene41904

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene41904.t1 MTR_7g088070 100.000 41 0 0 4 44 76 116 8.41e-24 89.7
MS.gene41904.t1 MTR_7g088070 100.000 37 0 0 4 40 76 112 1.33e-20 81.3
MS.gene41904.t1 MTR_2g027860 87.179 39 5 0 4 42 75 113 3.84e-17 72.8
MS.gene41904.t1 MTR_7g115530 81.081 37 7 0 4 40 244 280 1.26e-15 68.2
MS.gene41904.t1 MTR_7g115530 81.081 37 7 0 4 40 244 280 1.47e-15 68.2
MS.gene41904.t1 MTR_7g115530 81.081 37 7 0 4 40 244 280 1.62e-15 68.2
MS.gene41904.t1 MTR_7g115530 81.081 37 7 0 4 40 244 280 1.86e-15 68.2
MS.gene41904.t1 MTR_7g098250 73.810 42 10 1 4 45 288 328 1.04e-14 66.2
MS.gene41904.t1 MTR_1g053835 70.732 41 11 1 4 44 284 323 1.69e-14 65.5
MS.gene41904.t1 MTR_1g080330 80.556 36 7 0 4 39 201 236 2.29e-14 64.7
MS.gene41904.t1 MTR_1g080330 80.556 36 7 0 4 39 201 236 3.23e-14 64.7
MS.gene41904.t1 MTR_4g081710 66.667 42 13 1 4 44 43 84 3.93e-13 61.6
MS.gene41904.t1 MTR_7g093030 69.444 36 11 0 4 39 238 273 7.79e-13 60.5
MS.gene41904.t1 MTR_7g093030 69.444 36 11 0 4 39 238 273 9.47e-13 60.5
MS.gene41904.t1 MTR_2g086450 72.727 33 9 0 4 36 71 103 1.68e-12 59.7
MS.gene41904.t1 MTR_5g041350 74.194 31 8 0 4 34 41 71 6.39e-12 58.2
MS.gene41904.t1 MTR_6g032990 66.667 33 11 0 4 36 68 100 7.31e-12 58.2
MS.gene41904.t1 MTR_5g027440 71.875 32 9 0 4 35 51 82 2.07e-11 56.6
MS.gene41904.t1 MTR_1g090670 53.846 52 10 1 4 41 70 121 7.37e-11 55.1
MS.gene41904.t1 MTR_7g068600 61.364 44 14 1 4 44 39 82 7.48e-11 54.7
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene41904.t1 AT2G01060 87.805 41 5 0 4 44 41 81 1.05e-18 76.6
MS.gene41904.t1 AT4G28610 72.500 40 11 0 4 43 251 290 2.09e-14 65.5
MS.gene41904.t1 AT3G13040 80.000 35 7 0 4 38 267 301 3.56e-14 64.7
MS.gene41904.t1 AT3G13040 80.000 35 7 0 4 38 267 301 3.56e-14 64.7
MS.gene41904.t1 AT3G13040 80.000 35 7 0 4 38 267 301 3.56e-14 64.7
MS.gene41904.t1 AT5G29000 72.222 36 10 0 4 39 214 249 2.44e-13 62.4
MS.gene41904.t1 AT5G29000 72.222 36 10 0 4 39 214 249 2.44e-13 62.4
MS.gene41904.t1 AT5G29000 72.222 36 10 0 4 39 257 292 2.52e-13 62.4
MS.gene41904.t1 AT5G29000 72.222 36 10 0 4 39 257 292 2.65e-13 62.0
MS.gene41904.t1 AT5G06800 72.222 36 10 0 4 39 218 253 2.82e-13 61.6
MS.gene41904.t1 AT3G04450 66.667 39 13 0 4 42 264 302 3.63e-13 61.6
MS.gene41904.t1 AT3G04450 61.364 44 17 0 4 47 224 267 3.98e-13 61.6
MS.gene41904.t1 AT3G04450 61.364 44 17 0 4 47 224 267 3.98e-13 61.6
MS.gene41904.t1 AT3G04450 61.364 44 17 0 4 47 264 307 4.02e-13 61.6
MS.gene41904.t1 AT5G06800 72.222 36 10 0 4 39 218 253 4.24e-13 61.6
MS.gene41904.t1 AT2G20400 72.500 40 10 1 4 43 257 295 4.29e-13 61.6
MS.gene41904.t1 AT5G06800 72.222 36 10 0 4 39 218 253 5.24e-13 61.2
MS.gene41904.t1 AT2G20400 79.412 34 7 0 4 37 257 290 7.01e-13 60.8
MS.gene41904.t1 AT3G04030 72.727 33 9 0 4 36 71 103 1.05e-12 60.5
MS.gene41904.t1 AT3G04030 72.727 33 9 0 4 36 71 103 1.06e-12 60.5
MS.gene41904.t1 AT2G01060 84.375 32 5 0 13 44 1 32 1.64e-12 59.3
MS.gene41904.t1 AT5G18240 72.727 33 9 0 4 36 71 103 1.68e-12 60.1
MS.gene41904.t1 AT5G18240 72.727 33 9 0 4 36 71 103 1.68e-12 60.1
MS.gene41904.t1 AT5G18240 72.727 33 9 0 4 36 71 103 1.68e-12 60.1
MS.gene41904.t1 AT5G18240 72.727 33 9 0 4 36 71 103 1.68e-12 60.1
MS.gene41904.t1 AT5G18240 72.727 33 9 0 4 36 71 103 1.68e-12 60.1
MS.gene41904.t1 AT3G04030 71.875 32 9 0 5 36 71 102 4.01e-12 58.9
MS.gene41904.t1 AT1G69580 69.697 33 10 0 4 36 60 92 4.54e-12 58.5
MS.gene41904.t1 AT1G69580 69.697 33 10 0 4 36 60 92 4.55e-12 58.5
MS.gene41904.t1 AT3G12730 74.194 31 8 0 4 34 49 79 2.00e-11 56.2
MS.gene41904.t1 AT1G79430 64.103 39 14 0 4 42 60 98 3.99e-11 55.8

Find 16 sgRNAs with CRISPR-Local

Find 20 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TCATGTTAAAAGCCATTTAC+AGG 0.288705 7.4:+20244374 MS.gene41904:CDS
TTACCATCACCTGGTGATTC+AGG 0.291103 7.4:-20244522 None:intergenic
CACATATTGATACCTGTAAA+TGG 0.320680 7.4:-20244386 None:intergenic
CTGAGAGTGATGGGTGTGCC+TGG 0.409297 7.4:+20244339 MS.gene41904:CDS
ATCACTCTCAGAACACCTTT+CGG 0.429121 7.4:-20244327 None:intergenic
AACTTTAAATTATTCATGAT+AGG 0.430793 7.4:+20244297 None:intergenic
ATTCAGGCAAGTACTTCGCC+AGG 0.553148 7.4:-20244506 None:intergenic
CTACATGTAGAAGTATCGCC+TGG 0.558759 7.4:+20244488 MS.gene41904:intron
GAATCACCAGGTGATGGTAA+AGG 0.568026 7.4:+20244525 MS.gene41904:CDS
AAGTACTTGCCTGAATCACC+AGG 0.571352 7.4:+20244513 MS.gene41904:CDS
ACATGATAAATGGTCAGTCC+AGG 0.573039 7.4:-20244357 None:intergenic
ATGATAGGAGCAACACCGAA+AGG 0.616255 7.4:+20244312 MS.gene41904:CDS
TTGCCTGAATCACCAGGTGA+TGG 0.621799 7.4:+20244519 MS.gene41904:CDS
AAAGGTGTTCTGAGAGTGAT+GGG 0.625965 7.4:+20244330 MS.gene41904:CDS
GAAAGGTGTTCTGAGAGTGA+TGG 0.640082 7.4:+20244329 MS.gene41904:CDS
AAGGCACCTTTACCATCACC+TGG 0.649278 7.4:-20244531 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! AATATTTTACTAATTTTACA+TGG + chr7.4:20244438-20244457 MS.gene41904:intron 10.0%
!! TACATGTAGTGATATATAAT+AGG - chr7.4:20244477-20244496 None:intergenic 20.0%
!! ATGGCTTTTAACATGATAAA+TGG - chr7.4:20244370-20244389 None:intergenic 25.0%
CACATATTGATACCTGTAAA+TGG - chr7.4:20244389-20244408 None:intergenic 30.0%
CATTTACAGGTATCAATATG+TGG + chr7.4:20244387-20244406 MS.gene41904:intron 30.0%
TCATGTTAAAAGCCATTTAC+AGG + chr7.4:20244374-20244393 MS.gene41904:CDS 30.0%
ACATGATAAATGGTCAGTCC+AGG - chr7.4:20244360-20244379 None:intergenic 40.0%
ACGAAGCGCAAGAAAAAACA+AGG - chr7.4:20244553-20244572 None:intergenic 40.0%
ATCACTCTCAGAACACCTTT+CGG - chr7.4:20244330-20244349 None:intergenic 40.0%
!! AAAGGTGTTCTGAGAGTGAT+GGG + chr7.4:20244330-20244349 MS.gene41904:CDS 40.0%
AAGTACTTGCCTGAATCACC+AGG + chr7.4:20244513-20244532 MS.gene41904:CDS 45.0%
ATGATAGGAGCAACACCGAA+AGG + chr7.4:20244312-20244331 MS.gene41904:CDS 45.0%
TTACCATCACCTGGTGATTC+AGG - chr7.4:20244525-20244544 None:intergenic 45.0%
! GAATCACCAGGTGATGGTAA+AGG + chr7.4:20244525-20244544 MS.gene41904:CDS 45.0%
!! CTACATGTAGAAGTATCGCC+TGG + chr7.4:20244488-20244507 MS.gene41904:intron 45.0%
!! GAAAGGTGTTCTGAGAGTGA+TGG + chr7.4:20244329-20244348 MS.gene41904:CDS 45.0%
ATTCAGGCAAGTACTTCGCC+AGG - chr7.4:20244509-20244528 None:intergenic 50.0%
TTGCCTGAATCACCAGGTGA+TGG + chr7.4:20244519-20244538 MS.gene41904:CDS 50.0%
! AAGGCACCTTTACCATCACC+TGG - chr7.4:20244534-20244553 None:intergenic 50.0%
!! CTGAGAGTGATGGGTGTGCC+TGG + chr7.4:20244339-20244358 MS.gene41904:CDS 60.0%


Chromosome Type Strat End Strand Name
chr7.4 gene 20244312 20244581 20244312 ID=MS.gene41904
chr7.4 mRNA 20244312 20244581 20244312 ID=MS.gene41904.t1;Parent=MS.gene41904
chr7.4 exon 20244312 20244395 20244312 ID=MS.gene41904.t1.exon1;Parent=MS.gene41904.t1
chr7.4 CDS 20244312 20244395 20244312 ID=cds.MS.gene41904.t1;Parent=MS.gene41904.t1
chr7.4 exon 20244498 20244581 20244498 ID=MS.gene41904.t1.exon2;Parent=MS.gene41904.t1
chr7.4 CDS 20244498 20244581 20244498 ID=cds.MS.gene41904.t1;Parent=MS.gene41904.t1
Gene Sequence

>MS.gene41904

ATGATAGGAGCAACACCGAAAGGTGTTCTGAGAGTGATGGGTGTGCCTGGACTGACCATTTATCATGTTAAAAGCCATTTACAGGTATCAATATGTGGTCTAATTATTCTTTTGTGTATGTGCTACAATATTTTACTAATTTTACATGGATTCTAATTTTTTCCTATTATATATCACTACATGTAGAAGTATCGCCTGGCGAAGTACTTGCCTGAATCACCAGGTGATGGTAAAGGTGCCTTGTTTTTTCTTGCGCTTCGTAGTTCCTAA
Protein sequence

>MS.gene41904.t1

MIGATPKGVLRVMGVPGLTIYHVKSHLQKYRLAKYLPESPGDGKGALFFLALRSS