AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene26418

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene26418.t1 MTR_4g088035 80.000 120 23 1 1 119 1 120 2.59e-59 184
MS.gene26418.t1 MTR_3g071590 35.870 92 59 0 5 96 7 98 6.24e-17 72.4
MS.gene26418.t1 MTR_5g083230 33.333 96 64 0 1 96 1 96 5.62e-16 70.1
MS.gene26418.t1 MTR_6g011250 32.061 131 70 3 1 112 4 134 9.97e-16 69.7
MS.gene26418.t1 MTR_3g073690 34.021 97 64 0 3 99 6 102 2.34e-15 69.3
MS.gene26418.t1 MTR_4g083680 33.333 93 62 0 7 99 16 108 2.08e-14 66.2
MS.gene26418.t1 MTR_3g031660 29.032 93 66 0 4 96 5 97 3.28e-14 65.9
MS.gene26418.t1 MTR_2g068760 32.039 103 69 1 5 106 12 114 3.85e-14 65.1
MS.gene26418.t1 MTR_7g033800 31.633 98 67 0 3 100 8 105 9.30e-14 64.3
MS.gene26418.t1 MTR_4g105170 27.344 128 85 1 5 124 10 137 1.44e-12 61.6
MS.gene26418.t1 MTR_8g079580 31.683 101 61 2 7 99 9 109 1.49e-12 62.0
MS.gene26418.t1 MTR_6g011230 40.323 62 37 0 6 67 11 72 3.10e-12 60.8
MS.gene26418.t1 MTR_3g077240 31.579 95 65 0 5 99 9 103 5.94e-12 60.1
MS.gene26418.t1 MTR_6g005080 29.787 94 66 0 3 96 7 100 8.67e-12 58.5
MS.gene26418.t1 MTR_5g093010 27.835 97 63 1 7 96 6 102 1.24e-11 58.2
MS.gene26418.t1 MTR_1g095850 28.421 95 68 0 7 101 73 167 2.06e-11 58.9
MS.gene26418.t1 MTR_4g099230 29.167 120 73 4 6 113 2 121 2.56e-11 57.8
MS.gene26418.t1 MTR_6g005070 27.193 114 75 1 3 108 6 119 4.40e-11 57.0
MS.gene26418.t1 MTR_2g093310 28.866 97 69 0 5 101 32 128 4.69e-11 57.8
MS.gene26418.t1 MTR_7g028905 26.136 88 65 0 5 92 4 91 7.07e-11 55.8
MS.gene26418.t1 MTR_3g094690 30.303 99 66 1 5 100 46 144 7.07e-11 57.8
MS.gene26418.t1 MTR_2g100020 37.097 62 39 0 6 67 19 80 8.71e-11 57.8
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene26418.t1 AT1G06280 37.113 97 61 0 6 102 24 120 5.51e-18 76.3
MS.gene26418.t1 AT2G30130 32.258 93 63 0 4 96 6 98 5.50e-15 68.2
MS.gene26418.t1 AT3G26620 26.786 112 82 0 2 113 1 112 5.69e-14 63.9
MS.gene26418.t1 AT3G26660 26.786 112 82 0 2 113 1 112 6.20e-14 63.5
MS.gene26418.t1 AT3G50510 32.292 96 65 0 4 99 10 105 1.67e-13 64.3
MS.gene26418.t1 AT3G50510 32.292 96 65 0 4 99 10 105 1.67e-13 64.3
MS.gene26418.t1 AT5G15060 36.145 83 47 2 7 86 18 97 5.09e-13 62.0
MS.gene26418.t1 AT3G47870 32.143 84 57 0 6 89 36 119 1.87e-12 62.8
MS.gene26418.t1 AT1G16530 30.851 94 64 1 7 99 15 108 3.26e-12 60.1
MS.gene26418.t1 AT1G72980 42.857 63 36 0 5 67 12 74 6.75e-12 60.1
MS.gene26418.t1 AT3G27650 29.167 96 68 0 5 100 38 133 7.73e-12 59.3
MS.gene26418.t1 AT1G31320 29.545 88 62 0 5 92 12 99 1.28e-11 58.9
MS.gene26418.t1 AT5G63090 30.108 93 65 0 4 96 9 101 1.69e-11 58.9
MS.gene26418.t1 AT5G63090 30.108 93 65 0 4 96 9 101 1.69e-11 58.9
MS.gene26418.t1 AT5G63090 30.108 93 65 0 4 96 9 101 1.69e-11 58.9
MS.gene26418.t1 AT5G63090 30.108 93 65 0 4 96 9 101 1.69e-11 58.9

Find 21 sgRNAs with CRISPR-Local

Find 30 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ATTGAAAGAGAATGAAATTT+TGG 0.107789 4.4:+24792139 None:intergenic
ATCTTCTGACCCCAAATTTA+TGG 0.119750 4.4:-24792169 MS.gene26418:CDS
TTGGGCAAGACCCATAAATT+TGG 0.193828 4.4:+24792158 None:intergenic
TTCTTCTTCGTTGGATAATA+AGG 0.218223 4.4:+24792417 None:intergenic
TGGGCAAGACCCATAAATTT+GGG 0.299976 4.4:+24792159 None:intergenic
CACCAAGTGGACCATTGAAT+TGG 0.328762 4.4:+24792262 None:intergenic
TATTCTTGTTTCTTCTTCGT+TGG 0.359515 4.4:+24792408 None:intergenic
TCTTCTGACCCCAAATTTAT+GGG 0.360429 4.4:-24792168 MS.gene26418:CDS
ATAAATTTGGGGTCAGAAGA+TGG 0.471135 4.4:+24792171 None:intergenic
TTTGGTGTTGTCGTTGGAGT+AGG 0.480154 4.4:+24792199 None:intergenic
ACCAAGTGGACCATTGAATT+GGG 0.502431 4.4:+24792263 None:intergenic
ACCCAATTCAATGGTCCACT+TGG 0.513885 4.4:-24792264 MS.gene26418:CDS
GGTCAGAAGATGGAACAGTT+TGG 0.523150 4.4:+24792181 None:intergenic
GAACAGTTTGGTGTTGTCGT+TGG 0.529232 4.4:+24792193 None:intergenic
CTCAGAAACCTTGATGAACA+AGG 0.552123 4.4:-24792339 MS.gene26418:CDS
GGAAACAAGACCCAATTCAA+TGG 0.563084 4.4:-24792273 MS.gene26418:CDS
TTGATTGGGAAGCAAAGATG+TGG 0.575226 4.4:-24792294 MS.gene26418:CDS
TTCCCAATCAAAAGACTCGA+TGG 0.576338 4.4:+24792306 None:intergenic
TCGTTGGATAATAAGGAGCA+AGG 0.613164 4.4:+24792424 None:intergenic
GGGCAAGACCCATAAATTTG+GGG 0.616540 4.4:+24792160 None:intergenic
GCTTCAGTGAATGCACCAAG+TGG 0.660474 4.4:+24792249 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! AGTTTTTGGTTACAAAAAAT+TGG - chr4.4:24792256-24792275 MS.gene26418:CDS 20.0%
!!! ATTGAAAGAGAATGAAATTT+TGG + chr4.4:24792490-24792509 None:intergenic 20.0%
!!! TTGAAAGAGAATGAAATTTT+GGG + chr4.4:24792489-24792508 None:intergenic 20.0%
AACCAAAAACTTTGTGAACA+AGG + chr4.4:24792247-24792266 None:intergenic 30.0%
TTCTTCTTCGTTGGATAATA+AGG + chr4.4:24792212-24792231 None:intergenic 30.0%
! TATTCTTGTTTCTTCTTCGT+TGG + chr4.4:24792221-24792240 None:intergenic 30.0%
! TTTTTCTTCCTTGTTCATCA+AGG + chr4.4:24792298-24792317 None:intergenic 30.0%
!!! CTTTCATGCACTTTTTCTTT+TGG + chr4.4:24792175-24792194 None:intergenic 30.0%
!!! TTTTTCTTTTGGTGTCTACA+AGG + chr4.4:24792164-24792183 None:intergenic 30.0%
ATCTTCTGACCCCAAATTTA+TGG - chr4.4:24792457-24792476 MS.gene26418:CDS 35.0%
TCTTCTGACCCCAAATTTAT+GGG - chr4.4:24792458-24792477 MS.gene26418:CDS 35.0%
! ATAAATTTGGGGTCAGAAGA+TGG + chr4.4:24792458-24792477 None:intergenic 35.0%
! GACCTTGTTCACAAAGTTTT+TGG - chr4.4:24792242-24792261 MS.gene26418:CDS 35.0%
ACCAAGTGGACCATTGAATT+GGG + chr4.4:24792366-24792385 None:intergenic 40.0%
CTCAGAAACCTTGATGAACA+AGG - chr4.4:24792287-24792306 MS.gene26418:CDS 40.0%
GGAAACAAGACCCAATTCAA+TGG - chr4.4:24792353-24792372 MS.gene26418:CDS 40.0%
TCGTTGGATAATAAGGAGCA+AGG + chr4.4:24792205-24792224 None:intergenic 40.0%
TGGGCAAGACCCATAAATTT+GGG + chr4.4:24792470-24792489 None:intergenic 40.0%
TTCCCAATCAAAAGACTCGA+TGG + chr4.4:24792323-24792342 None:intergenic 40.0%
TTGATTGGGAAGCAAAGATG+TGG - chr4.4:24792332-24792351 MS.gene26418:CDS 40.0%
TTGGGCAAGACCCATAAATT+TGG + chr4.4:24792471-24792490 None:intergenic 40.0%
! AAGCCATCGAGTCTTTTGAT+TGG - chr4.4:24792317-24792336 MS.gene26418:CDS 40.0%
!! AGCCATCGAGTCTTTTGATT+GGG - chr4.4:24792318-24792337 MS.gene26418:CDS 40.0%
ACCCAATTCAATGGTCCACT+TGG - chr4.4:24792362-24792381 MS.gene26418:CDS 45.0%
CACCAAGTGGACCATTGAAT+TGG + chr4.4:24792367-24792386 None:intergenic 45.0%
GGGCAAGACCCATAAATTTG+GGG + chr4.4:24792469-24792488 None:intergenic 45.0%
GGTCAGAAGATGGAACAGTT+TGG + chr4.4:24792448-24792467 None:intergenic 45.0%
!! GAACAGTTTGGTGTTGTCGT+TGG + chr4.4:24792436-24792455 None:intergenic 45.0%
!! TTTGGTGTTGTCGTTGGAGT+AGG + chr4.4:24792430-24792449 None:intergenic 45.0%
GCTTCAGTGAATGCACCAAG+TGG + chr4.4:24792380-24792399 None:intergenic 50.0%


Chromosome Type Strat End Strand Name
chr4.4 gene 24792137 24792511 24792137 ID=MS.gene26418
chr4.4 mRNA 24792137 24792511 24792137 ID=MS.gene26418.t1;Parent=MS.gene26418
chr4.4 exon 24792137 24792511 24792137 ID=MS.gene26418.t1.exon1;Parent=MS.gene26418.t1
chr4.4 CDS 24792137 24792511 24792137 ID=cds.MS.gene26418.t1;Parent=MS.gene26418.t1
Gene Sequence

>MS.gene26418

ATGATAAACAAGACAGCATGTGCTCCTTGTAGACACCAAAAGAAAAAGTGCATGAAAGATTGCTTCCTTGCTCCTTATTATCCAACGAAGAAGAAACAAGAATACGACCTTGTTCACAAAGTTTTTGGTTACAAAAAATTGGAAAAAATGCTCAGAAACCTTGATGAACAAGGAAGAAAAAAGCCATCGAGTCTTTTGATTGGGAAGCAAAGATGTGGAAACAAGACCCAATTCAATGGTCCACTTGGTGCATTCACTGAAGCTCAGAATGAAATAGCACGACTACAAAACCTACTCCAACGACAACACCAAACTGTTCCATCTTCTGACCCCAAATTTATGGGTCTTGCCCAAAATTTCATTCTCTTTCAATAG
Protein sequence

>MS.gene26418.t1

MINKTACAPCRHQKKKCMKDCFLAPYYPTKKKQEYDLVHKVFGYKKLEKMLRNLDEQGRKKPSSLLIGKQRCGNKTQFNGPLGAFTEAQNEIARLQNLLQRQHQTVPSSDPKFMGLAQNFILFQ