AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene60898

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene60898.t1 MTR_2g062600 97.345 113 3 0 1 113 1 113 5.30e-73 213
MS.gene60898.t1 MTR_4g428370 45.133 113 60 2 1 112 58 169 1.48e-25 94.4
MS.gene60898.t1 MTR_4g027800 41.593 113 64 2 1 112 1 112 4.55e-23 86.7
MS.gene60898.t1 MTR_4g027840 41.593 113 64 2 1 112 1 112 4.59e-23 87.0
MS.gene60898.t1 MTR_4g028180 37.288 118 68 2 1 112 6 123 3.53e-21 82.0
MS.gene60898.t1 MTR_4g029390 38.095 105 63 2 9 112 10 113 9.12e-21 80.5
MS.gene60898.t1 MTR_4g029350 39.815 108 62 3 6 112 8 113 5.96e-19 75.9
MS.gene60898.t1 MTR_7g073170 34.615 104 68 0 10 113 13 116 8.59e-19 75.9
MS.gene60898.t1 MTR_4g029210 36.607 112 65 4 6 113 4 113 6.38e-18 73.6
MS.gene60898.t1 MTR_7g073130 37.168 113 68 1 1 113 7 116 2.91e-17 72.0
MS.gene60898.t1 MTR_4g028190 29.907 107 74 1 8 113 13 119 2.77e-16 69.3
MS.gene60898.t1 MTR_7g073150 30.172 116 77 2 1 112 1 116 4.28e-16 69.3
MS.gene60898.t1 MTR_7g073120 33.913 115 71 3 1 113 8 119 1.15e-15 68.6
MS.gene60898.t1 MTR_7g072900 34.211 114 71 2 1 113 7 117 5.50e-14 63.2
MS.gene60898.t1 MTR_1g040335 36.283 113 68 2 2 113 8 117 5.89e-14 63.2
MS.gene60898.t1 MTR_7g072930 32.000 100 67 1 14 112 17 116 6.05e-14 63.9
MS.gene60898.t1 MTR_7g072730 31.193 109 73 2 6 112 9 117 7.36e-14 64.3
MS.gene60898.t1 MTR_7g072830 32.174 115 73 3 1 113 7 118 2.69e-13 61.6
MS.gene60898.t1 MTR_4g028310 30.172 116 78 2 1 113 1 116 4.10e-13 61.6
MS.gene60898.t1 MTR_7g072980 34.783 115 70 3 1 113 7 118 1.07e-12 60.5
MS.gene60898.t1 MTR_7g451500 31.868 91 61 1 24 113 7 97 1.75e-12 58.9
MS.gene60898.t1 MTR_3g467100 27.778 108 74 3 8 113 7 112 1.76e-12 59.3
MS.gene60898.t1 MTR_7g072810 33.043 115 66 4 1 113 7 112 2.36e-11 56.6
MS.gene60898.t1 MTR_3g056640 25.424 118 82 3 1 112 2 119 4.39e-11 55.8
MS.gene60898.t1 MTR_7g073100 33.333 114 72 2 1 113 7 117 4.41e-11 56.6
MS.gene60898.t1 MTR_7g072760 32.692 104 68 2 12 113 17 120 5.38e-11 55.8
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene60898.t1 AT2G18370 53.271 107 50 0 6 112 7 113 8.58e-37 121
MS.gene60898.t1 AT5G59320 41.593 113 64 2 1 112 1 112 2.92e-22 84.3
MS.gene60898.t1 AT5G59310 36.607 112 68 2 1 112 1 109 8.66e-21 80.5
MS.gene60898.t1 AT3G51590 39.216 102 60 2 11 111 12 112 9.30e-19 75.5
MS.gene60898.t1 AT5G01870 39.048 105 60 2 11 112 10 113 3.98e-18 73.9
MS.gene60898.t1 AT3G08770 39.785 93 52 2 22 111 18 109 3.71e-17 71.2
MS.gene60898.t1 AT3G08770 39.785 93 52 2 22 111 18 109 4.32e-17 71.2
MS.gene60898.t1 AT2G38540 34.513 113 69 3 1 111 5 114 1.81e-15 67.4
MS.gene60898.t1 AT4G33355 35.577 104 64 3 11 113 16 117 2.24e-15 67.0
MS.gene60898.t1 AT2G15050 32.407 108 67 3 3 104 2 109 3.15e-15 66.6
MS.gene60898.t1 AT2G15050 32.407 108 67 3 3 104 2 109 3.16e-15 66.6
MS.gene60898.t1 AT2G15050 32.407 108 67 3 3 104 2 109 3.34e-15 66.6
MS.gene60898.t1 AT4G33355 35.922 103 63 3 11 112 16 116 8.86e-15 65.5
MS.gene60898.t1 AT3G51600 33.333 114 70 3 4 112 3 115 2.12e-14 64.3

Find 24 sgRNAs with CRISPR-Local

Find 25 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TGCAATTAAAGAAGATTTCA+TGG 0.285915 2.3:+31866492 None:intergenic
GAAACCTTGTGTGAGCTATT+TGG 0.286149 2.3:-31866389 MS.gene60898:CDS
CAATTGGCTCAGGCTCTTGC+AGG 0.325545 2.3:-31866229 MS.gene60898:CDS
AATTGAAGCCTCTGAATTAG+AGG 0.347310 2.3:+31866438 None:intergenic
TACTTGGAACAATCAGCATC+TGG 0.351088 2.3:+31866172 None:intergenic
CCACCAGCTGCATGTTGCTC+TGG 0.359411 2.3:-31866349 MS.gene60898:CDS
AGCTATTTGGTTAGTGGAAG+TGG 0.442124 2.3:-31866376 MS.gene60898:CDS
TATTAAAATCAACTCACAAT+TGG 0.472842 2.3:-31866245 MS.gene60898:CDS
TGTGTGAGCTATTTGGTTAG+TGG 0.472934 2.3:-31866382 MS.gene60898:CDS
CTTTGTTGCCTCTAATTCAG+AGG 0.498312 2.3:-31866446 MS.gene60898:CDS
TTCATGCAGTGATGTGATCA+AGG 0.499471 2.3:-31866416 MS.gene60898:CDS
AATCAACTCACAATTGGCTC+AGG 0.514463 2.3:-31866239 MS.gene60898:CDS
ACTTGGAACAATCAGCATCT+GGG 0.519962 2.3:+31866173 None:intergenic
GCTCCAGAGCAACATGCAGC+TGG 0.542595 2.3:+31866346 None:intergenic
CAGGCTCTTGCAGGGAACTG+TGG 0.566184 2.3:-31866220 MS.gene60898:CDS
CCAGAGCAACATGCAGCTGG+TGG 0.571454 2.3:+31866349 None:intergenic
AGCATCTGGGGAGATACTGA+TGG 0.572323 2.3:+31866186 None:intergenic
GCATCTGGGGAGATACTGAT+GGG 0.583176 2.3:+31866187 None:intergenic
AATTGGCTCAGGCTCTTGCA+GGG 0.601314 2.3:-31866228 MS.gene60898:CDS
CTTGGAACAATCAGCATCTG+GGG 0.606095 2.3:+31866174 None:intergenic
ATCAGCTGTATCAACATCTG+AGG 0.641164 2.3:-31866311 MS.gene60898:CDS
CTAACCAAATAGCTCACACA+AGG 0.649954 2.3:+31866385 None:intergenic
ATCTGGGGAGATACTGATGG+GGG 0.675132 2.3:+31866189 None:intergenic
CATCTGGGGAGATACTGATG+GGG 0.712150 2.3:+31866188 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TATTAAAATCAACTCACAAT+TGG - chr2.3:31866416-31866435 MS.gene60898:CDS 20.0%
!!! TGAGTTGATTTTAATACTCT+TGG + chr2.3:31866412-31866431 None:intergenic 25.0%
!! GATTTTAATACTCTTGGAAG+TGG + chr2.3:31866406-31866425 None:intergenic 30.0%
AATTGAAGCCTCTGAATTAG+AGG + chr2.3:31866226-31866245 None:intergenic 35.0%
ACTTGGAACAATCAGCATCT+GGG + chr2.3:31866491-31866510 None:intergenic 40.0%
AGCTATTTGGTTAGTGGAAG+TGG - chr2.3:31866285-31866304 MS.gene60898:CDS 40.0%
ATCAGCTGTATCAACATCTG+AGG - chr2.3:31866350-31866369 MS.gene60898:CDS 40.0%
CTAACCAAATAGCTCACACA+AGG + chr2.3:31866279-31866298 None:intergenic 40.0%
CTTTGTTGCCTCTAATTCAG+AGG - chr2.3:31866215-31866234 MS.gene60898:CDS 40.0%
GAAACCTTGTGTGAGCTATT+TGG - chr2.3:31866272-31866291 MS.gene60898:CDS 40.0%
TACTTGGAACAATCAGCATC+TGG + chr2.3:31866492-31866511 None:intergenic 40.0%
TGTGTGAGCTATTTGGTTAG+TGG - chr2.3:31866279-31866298 MS.gene60898:CDS 40.0%
TTCATGCAGTGATGTGATCA+AGG - chr2.3:31866245-31866264 MS.gene60898:CDS 40.0%
! AATCAACTCACAATTGGCTC+AGG - chr2.3:31866422-31866441 MS.gene60898:CDS 40.0%
CTTGGAACAATCAGCATCTG+GGG + chr2.3:31866490-31866509 None:intergenic 45.0%
AGCATCTGGGGAGATACTGA+TGG + chr2.3:31866478-31866497 None:intergenic 50.0%
ATCTGGGGAGATACTGATGG+GGG + chr2.3:31866475-31866494 None:intergenic 50.0%
CATCTGGGGAGATACTGATG+GGG + chr2.3:31866476-31866495 None:intergenic 50.0%
GCATCTGGGGAGATACTGAT+GGG + chr2.3:31866477-31866496 None:intergenic 50.0%
! AATTGGCTCAGGCTCTTGCA+GGG - chr2.3:31866433-31866452 MS.gene60898:CDS 50.0%
! CAATTGGCTCAGGCTCTTGC+AGG - chr2.3:31866432-31866451 MS.gene60898:CDS 55.0%
CAGGCTCTTGCAGGGAACTG+TGG - chr2.3:31866441-31866460 MS.gene60898:CDS 60.0%
CCACCAGCTGCATGTTGCTC+TGG - chr2.3:31866312-31866331 MS.gene60898:CDS 60.0%
CCAGAGCAACATGCAGCTGG+TGG + chr2.3:31866315-31866334 None:intergenic 60.0%
GCTCCAGAGCAACATGCAGC+TGG + chr2.3:31866318-31866337 None:intergenic 60.0%


Chromosome Type Strat End Strand Name
chr2.3 gene 31866171 31866512 31866171 ID=MS.gene60898
chr2.3 mRNA 31866171 31866512 31866171 ID=MS.gene60898.t1;Parent=MS.gene60898
chr2.3 exon 31866171 31866512 31866171 ID=MS.gene60898.t1.exon1;Parent=MS.gene60898.t1
chr2.3 CDS 31866171 31866512 31866171 ID=cds.MS.gene60898.t1;Parent=MS.gene60898.t1
Gene Sequence

>MS.gene60898

ATGAAATCTTCTTTAATTGCATTTGCTGCTCTTGTGCTTCTGATCTTTGTTGCCTCTAATTCAGAGGCTTCAATTTCATGCAGTGATGTGATCAAGGACTTGAAACCTTGTGTGAGCTATTTGGTTAGTGGAAGTGGACAGCCACCAGCTGCATGTTGCTCTGGAGCTAAAGCTCTTGCATCAGCTGTATCAACATCTGAGGATAAAAAAGCTGCTTGCAACTGCATCAAATCCACTTCCAAGAGTATTAAAATCAACTCACAATTGGCTCAGGCTCTTGCAGGGAACTGTGGAATTAACACCCCCATCAGTATCTCCCCAGATGCTGATTGTTCCAAGTAA
Protein sequence

>MS.gene60898.t1

MKSSLIAFAALVLLIFVASNSEASISCSDVIKDLKPCVSYLVSGSGQPPAACCSGAKALASAVSTSEDKKAACNCIKSTSKSIKINSQLAQALAGNCGINTPISISPDADCSK