AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene060728


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene060728.t1 MTR_4g115075 92.708 192 13 1 9 200 1 191 6.87e-109 310
MS.gene060728.t1 MTR_3g106850 31.373 204 116 8 9 200 1 192 9.12e-24 94.0
MS.gene060728.t1 MTR_1g069495 30.719 153 53 4 101 200 83 235 6.64e-15 71.6
MS.gene060728.t1 MTR_1g070520 28.723 188 95 7 42 200 35 212 6.09e-13 65.9
MS.gene060728.t1 MTR_1g093240 26.351 148 85 3 75 200 58 203 2.10e-12 63.5
MS.gene060728.t1 MTR_1g076270 26.490 151 77 5 70 200 21 157 2.13e-12 63.2
MS.gene060728.t1 MTR_1g093350 26.490 151 77 5 70 200 21 157 2.13e-12 63.2
MS.gene060728.t1 MTR_1g080860 32.168 143 65 6 86 200 82 220 4.50e-12 63.2
MS.gene060728.t1 MTR_1g093240 26.351 148 85 3 75 200 58 203 4.91e-12 63.2
MS.gene060728.t1 MTR_1g093240 26.351 148 85 3 75 200 58 203 5.58e-12 62.8
MS.gene060728.t1 MTR_1g080860 32.168 143 65 6 86 200 82 220 5.61e-12 63.2
MS.gene060728.t1 MTR_4g124300 32.727 110 53 4 99 200 70 166 3.15e-11 60.1
MS.gene060728.t1 MTR_2g100780 27.465 142 60 3 101 200 97 237 3.59e-11 61.2
MS.gene060728.t1 MTR_2g100780 27.465 142 60 3 101 200 97 237 5.43e-11 60.5
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene060728.t1 AT4G32280 29.004 231 120 8 9 200 1 226 1.26e-22 92.0
MS.gene060728.t1 AT4G32280 48.485 66 31 1 138 200 119 184 5.24e-17 76.3
MS.gene060728.t1 AT1G04550 35.338 133 53 4 101 200 70 202 7.48e-17 76.3
MS.gene060728.t1 AT5G25890 32.061 131 83 2 72 200 20 146 1.16e-15 72.0
MS.gene060728.t1 AT2G33310 30.216 139 53 4 101 200 77 210 2.67e-14 69.7
MS.gene060728.t1 AT2G33310 30.216 139 53 4 101 200 76 209 2.80e-14 69.3
MS.gene060728.t1 AT2G33310 30.216 139 53 4 101 200 76 209 2.80e-14 69.3
MS.gene060728.t1 AT5G43700 30.328 122 67 3 87 200 49 160 5.31e-14 67.8
MS.gene060728.t1 AT1G04240 31.452 124 67 3 86 200 150 264 1.73e-13 67.8
MS.gene060728.t1 AT1G04240 31.452 124 67 3 86 200 50 164 2.05e-13 66.2
MS.gene060728.t1 AT4G32280 26.471 204 109 7 9 176 1 199 5.10e-13 65.1
MS.gene060728.t1 AT4G28640 29.545 132 61 3 101 200 89 220 5.40e-13 65.9
MS.gene060728.t1 AT4G28640 29.545 132 61 3 101 200 89 220 6.58e-13 65.9
MS.gene060728.t1 AT4G28640 29.545 132 61 3 101 200 89 220 1.15e-12 65.5
MS.gene060728.t1 AT4G14550 29.752 121 62 2 101 200 77 195 3.63e-12 62.8
MS.gene060728.t1 AT4G14550 29.752 121 62 2 101 200 77 195 7.05e-12 62.8
MS.gene060728.t1 AT4G14550 29.752 121 62 2 101 200 77 195 7.50e-12 62.4
MS.gene060728.t1 AT3G15540 33.645 107 54 2 101 200 71 167 2.34e-11 60.8

Find 47 sgRNAs with CRISPR-Local

Find 56 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TCTCTTTGAATCATGATAAT+AGG 0.233271 8.2:+13592205 MS.gene060728:CDS
TCTGAGTGGCCAGGAGTTAA+TGG 0.256229 8.2:-13592297 None:intergenic
CAAACATGTCCATCAAAGTT+TGG 0.287284 8.2:-13592705 None:intergenic
TACTCTCAACCAAACTTTGA+TGG 0.301864 8.2:+13592696 MS.gene060728:CDS
TCACAATATGGAGCTTCATT+TGG 0.317095 8.2:+13592119 MS.gene060728:CDS
CTCTCTACACAATCACAATA+TGG 0.343546 8.2:+13592107 MS.gene060728:CDS
GAGAGAAAGAGTGGGAAGGT+TGG 0.357245 8.2:-13592271 None:intergenic
CACAATATGGAGCTTCATTT+GGG 0.385933 8.2:+13592120 MS.gene060728:CDS
ATCAAGACAAAGAAGGTGAT+TGG 0.388129 8.2:+13592885 MS.gene060728:CDS
TTCTTCCTCCTACAATTAAC+CGG 0.390508 8.2:-13592529 None:intergenic
TTCTTGCTCAAGATATTTCA+TGG 0.399762 8.2:+13592909 MS.gene060728:CDS
GATGGCCTCCGGTTAATTGT+AGG 0.427386 8.2:+13592521 MS.gene060728:CDS
GATCACGTGGTCCCCATTGA+TGG 0.439591 8.2:+13592580 MS.gene060728:CDS
CTGAGTGGCCAGGAGTTAAT+GGG 0.451365 8.2:-13592296 None:intergenic
GATGATGAAGAAGCTCTTGT+TGG 0.454535 8.2:+13592499 MS.gene060728:CDS
TAATGGGAGGAGAGAAAGAG+TGG 0.454609 8.2:-13592280 None:intergenic
TCTCTCCTCCCATTAACTCC+TGG 0.458165 8.2:+13592288 MS.gene060728:CDS
AGAAAGAGTGGGAAGGTTGG+TGG 0.462033 8.2:-13592268 None:intergenic
ATGGTTCTCATGATAATCAT+AGG 0.480012 8.2:+13592599 MS.gene060728:CDS
ATTATCATGAGAACCATCAA+TGG 0.488136 8.2:-13592593 None:intergenic
AGCTCTTGTTGGATGGCCTC+CGG 0.493311 8.2:+13592510 MS.gene060728:CDS
TTACTTGGTGATGGTGGTAG+TGG 0.498349 8.2:-13592358 None:intergenic
TGATCAACAACAGTATGAAC+TGG 0.501567 8.2:+13592859 MS.gene060728:CDS
GAATTACGTGAAGGTGAAGA+TGG 0.506755 8.2:+13592621 MS.gene060728:CDS
TTATCATGAGAACCATCAAT+GGG 0.508335 8.2:-13592592 None:intergenic
TATTAATTACTTGGTGATGG+TGG 0.510150 8.2:-13592364 None:intergenic
TAATATTAATTACTTGGTGA+TGG 0.522964 8.2:-13592367 None:intergenic
CGGACGAGAATTATTATAAG+TGG 0.529450 8.2:-13592154 None:intergenic
CTGGTTTATCAAGACAAAGA+AGG 0.557412 8.2:+13592878 MS.gene060728:CDS
GGTTGAGAGTATGAAATGAA+TGG 0.558722 8.2:-13592684 None:intergenic
TCATGATCATCTGAGTGGCC+AGG 0.559365 8.2:-13592306 None:intergenic
TACGTGAAGGTGAAGATGGA+AGG 0.560134 8.2:+13592625 MS.gene060728:CDS
GGAGGAGAGAAAGAGTGGGA+AGG 0.576479 8.2:-13592275 None:intergenic
AATGGGAGGAGAGAAAGAGT+GGG 0.579242 8.2:-13592279 None:intergenic
ATGAAGAAGCTCTTGTTGGA+TGG 0.580018 8.2:+13592503 MS.gene060728:CDS
TATCATGATTCAAAGAGAAG+TGG 0.584987 8.2:-13592200 None:intergenic
GGCCTCCGGTTAATTGTAGG+AGG 0.613414 8.2:+13592524 MS.gene060728:CDS
AGGTGTAGGAATAGCTCGAA+AGG 0.621460 8.2:+13592645 MS.gene060728:CDS
TTAGTAGCAGCAATATCGTA+CGG 0.636596 8.2:-13592174 None:intergenic
AAGGTGAAGATGGAAGGTGT+AGG 0.649720 8.2:+13592631 MS.gene060728:CDS
TTCCTCCTACAATTAACCGG+AGG 0.665193 8.2:-13592526 None:intergenic
TAATCATAGGAATTACGTGA+AGG 0.675805 8.2:+13592612 MS.gene060728:CDS
AGTGGCCAGGAGTTAATGGG+AGG 0.697461 8.2:-13592293 None:intergenic
TTGCTCAAGATATTTCATGG+AGG 0.720826 8.2:+13592912 MS.gene060728:CDS
CATGATCATGATCATCTGAG+TGG 0.721603 8.2:-13592311 None:intergenic
AAATGATGTTGAAGATCACG+TGG 0.746908 8.2:+13592567 MS.gene060728:CDS
TATCATGAGAACCATCAATG+GGG 0.763816 8.2:-13592591 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AACTAATAATATTAATTACT+TGG - chr8.2:13592376-13592395 None:intergenic 10.0%
!! GTACATTAATATTATTTATA+TGG + chr8.2:13592430-13592449 MS.gene060728:intron 10.0%
!!! ATTAGTAGTACTAATTATTT+TGG - chr8.2:13592772-13592791 None:intergenic 15.0%
!! AAGTACTAACATTGAAATAT+TGG - chr8.2:13592404-13592423 None:intergenic 20.0%
!!! TAATATTAATTACTTGGTGA+TGG - chr8.2:13592370-13592389 None:intergenic 20.0%
! GTATATATAGTGTATATGCA+CGG + chr8.2:13592800-13592819 MS.gene060728:intron 25.0%
! TCTCTTTGAATCATGATAAT+AGG + chr8.2:13592205-13592224 MS.gene060728:CDS 25.0%
! TTAGTACTACTAATTAGTTG+AGG + chr8.2:13592778-13592797 MS.gene060728:intron 25.0%
ATGGTTCTCATGATAATCAT+AGG + chr8.2:13592599-13592618 MS.gene060728:CDS 30.0%
ATTATCATGAGAACCATCAA+TGG - chr8.2:13592596-13592615 None:intergenic 30.0%
TAATCATAGGAATTACGTGA+AGG + chr8.2:13592612-13592631 MS.gene060728:CDS 30.0%
TATCATGATTCAAAGAGAAG+TGG - chr8.2:13592203-13592222 None:intergenic 30.0%
TCATGTAGTTGGAAATTAAC+AGG + chr8.2:13592830-13592849 MS.gene060728:intron 30.0%
TTATCATGAGAACCATCAAT+GGG - chr8.2:13592595-13592614 None:intergenic 30.0%
TTCTTGCTCAAGATATTTCA+TGG + chr8.2:13592909-13592928 MS.gene060728:CDS 30.0%
!! TATTAATTACTTGGTGATGG+TGG - chr8.2:13592367-13592386 None:intergenic 30.0%
AAATGATGTTGAAGATCACG+TGG + chr8.2:13592567-13592586 MS.gene060728:CDS 35.0%
ACGGCATTAATTCATGTAGT+TGG + chr8.2:13592819-13592838 MS.gene060728:intron 35.0%
ATCAAGACAAAGAAGGTGAT+TGG + chr8.2:13592885-13592904 MS.gene060728:CDS 35.0%
CAAACATGTCCATCAAAGTT+TGG - chr8.2:13592708-13592727 None:intergenic 35.0%
CACAATATGGAGCTTCATTT+GGG + chr8.2:13592120-13592139 MS.gene060728:CDS 35.0%
CGGACGAGAATTATTATAAG+TGG - chr8.2:13592157-13592176 None:intergenic 35.0%
CTCTCTACACAATCACAATA+TGG + chr8.2:13592107-13592126 MS.gene060728:CDS 35.0%
CTGGTTTATCAAGACAAAGA+AGG + chr8.2:13592878-13592897 MS.gene060728:CDS 35.0%
TACTCTCAACCAAACTTTGA+TGG + chr8.2:13592696-13592715 MS.gene060728:CDS 35.0%
TATCATGAGAACCATCAATG+GGG - chr8.2:13592594-13592613 None:intergenic 35.0%
TCACAATATGGAGCTTCATT+TGG + chr8.2:13592119-13592138 MS.gene060728:CDS 35.0%
TGATCAACAACAGTATGAAC+TGG + chr8.2:13592859-13592878 MS.gene060728:CDS 35.0%
TTAGTAGCAGCAATATCGTA+CGG - chr8.2:13592177-13592196 None:intergenic 35.0%
TTCTTCCTCCTACAATTAAC+CGG - chr8.2:13592532-13592551 None:intergenic 35.0%
! ACGTAGTTTTTCTCAACTCT+TGG + chr8.2:13592230-13592249 MS.gene060728:CDS 35.0%
! GGTTGAGAGTATGAAATGAA+TGG - chr8.2:13592687-13592706 None:intergenic 35.0%
ATGAAGAAGCTCTTGTTGGA+TGG + chr8.2:13592503-13592522 MS.gene060728:CDS 40.0%
CATGATCATGATCATCTGAG+TGG - chr8.2:13592314-13592333 None:intergenic 40.0%
GAATTACGTGAAGGTGAAGA+TGG + chr8.2:13592621-13592640 MS.gene060728:CDS 40.0%
GATGATGAAGAAGCTCTTGT+TGG + chr8.2:13592499-13592518 MS.gene060728:CDS 40.0%
AATGGGAGGAGAGAAAGAGT+GGG - chr8.2:13592282-13592301 None:intergenic 45.0%
AGGTGTAGGAATAGCTCGAA+AGG + chr8.2:13592645-13592664 MS.gene060728:CDS 45.0%
TAATGGGAGGAGAGAAAGAG+TGG - chr8.2:13592283-13592302 None:intergenic 45.0%
TACGTGAAGGTGAAGATGGA+AGG + chr8.2:13592625-13592644 MS.gene060728:CDS 45.0%
TTCCTCCTACAATTAACCGG+AGG - chr8.2:13592529-13592548 None:intergenic 45.0%
! AAGGTGAAGATGGAAGGTGT+AGG + chr8.2:13592631-13592650 MS.gene060728:CDS 45.0%
!! TTACTTGGTGATGGTGGTAG+TGG - chr8.2:13592361-13592380 None:intergenic 45.0%
!!! TTAATTTATTTGTTTAATTT+AGG + chr8.2:13592467-13592486 MS.gene060728:intron 5.0%
AGAAAGAGTGGGAAGGTTGG+TGG - chr8.2:13592271-13592290 None:intergenic 50.0%
CTGAGTGGCCAGGAGTTAAT+GGG - chr8.2:13592299-13592318 None:intergenic 50.0%
GAGAGAAAGAGTGGGAAGGT+TGG - chr8.2:13592274-13592293 None:intergenic 50.0%
GATGGCCTCCGGTTAATTGT+AGG + chr8.2:13592521-13592540 MS.gene060728:CDS 50.0%
TCATGATCATCTGAGTGGCC+AGG - chr8.2:13592309-13592328 None:intergenic 50.0%
TCTCTCCTCCCATTAACTCC+TGG + chr8.2:13592288-13592307 MS.gene060728:CDS 50.0%
TCTGAGTGGCCAGGAGTTAA+TGG - chr8.2:13592300-13592319 None:intergenic 50.0%
AGCTCTTGTTGGATGGCCTC+CGG + chr8.2:13592510-13592529 MS.gene060728:CDS 55.0%
AGTGGCCAGGAGTTAATGGG+AGG - chr8.2:13592296-13592315 None:intergenic 55.0%
GATCACGTGGTCCCCATTGA+TGG + chr8.2:13592580-13592599 MS.gene060728:CDS 55.0%
GGAGGAGAGAAAGAGTGGGA+AGG - chr8.2:13592278-13592297 None:intergenic 55.0%
GGCCTCCGGTTAATTGTAGG+AGG + chr8.2:13592524-13592543 MS.gene060728:CDS 55.0%


Chromosome Type Strat End Strand Name
chr8.2 gene 13592102 13592933 13592102 ID=MS.gene060728
chr8.2 mRNA 13592102 13592933 13592102 ID=MS.gene060728.t1;Parent=MS.gene060728
chr8.2 exon 13592102 13592376 13592102 ID=MS.gene060728.t1.exon1;Parent=MS.gene060728.t1
chr8.2 CDS 13592102 13592376 13592102 ID=cds.MS.gene060728.t1;Parent=MS.gene060728.t1
chr8.2 exon 13592489 13592733 13592489 ID=MS.gene060728.t1.exon2;Parent=MS.gene060728.t1
chr8.2 CDS 13592489 13592733 13592489 ID=cds.MS.gene060728.t1;Parent=MS.gene060728.t1
chr8.2 exon 13592852 13592933 13592852 ID=MS.gene060728.t1.exon3;Parent=MS.gene060728.t1
chr8.2 CDS 13592852 13592933 13592852 ID=cds.MS.gene060728.t1;Parent=MS.gene060728.t1
Gene Sequence

>MS.gene060728

CTTATCTCTCTACACAATCACAATATGGAGCTTCATTTGGGTCTTGCTCTCTCCACTTATAATAATTCTCGTCCGTACGATATTGCTGCTACTAATAGCCACTTCTCTTTGAATCATGATAATAGGAAACGTAGTTTTTCTCAACTCTTGGAGCATGCAGCAGAAACCACCAACCTTCCCACTCTTTCTCTCCTCCCATTAACTCCTGGCCACTCAGATGATCATGATCATGATGATCAACACTGCTCTCACAGCTCCACTACCACCATCACCAAGTAATTAATATTATTAGTTACTCTCCAATATTTCAATGTTAGTACTTAGTATAGTACATTAATATTATTTATATGGTATATTGAATATTATTAATTTATTTGTTTAATTTAGGAGCAATGAAGATGATGAAGAAGCTCTTGTTGGATGGCCTCCGGTTAATTGTAGGAGGAAGAAAATTCGTTCTAATGAAAATGATGTTGAAGATCACGTGGTCCCCATTGATGGTTCTCATGATAATCATAGGAATTACGTGAAGGTGAAGATGGAAGGTGTAGGAATAGCTCGAAAGGTTAATCTTAGCATGCACCATTCATTTCATACTCTCAACCAAACTTTGATGGACATGTTTGAAAAATGTACGTCTTCTTTATTCAAATTTCTAATTAAATTTCCAAAATAATTAGTACTACTAATTAGTTGAGGTATATATAGTGTATATGCACGGCATTAATTCATGTAGTTGGAAATTAACAGGTGATCATGATCAACAACAGTATGAACTGGTTTATCAAGACAAAGAAGGTGATTGGCTTCTTGCTCAAGATATTTCATGGAG

Protein sequence

>MS.gene060728.t1

LISLHNHNMELHLGLALSTYNNSRPYDIAATNSHFSLNHDNRKRSFSQLLEHAAETTNLPTLSLLPLTPGHSDDHDHDDQHCSHSSTTTITKSNEDDEEALVGWPPVNCRRKKIRSNENDVEDHVVPIDGSHDNHRNYVKVKMEGVGIARKVNLSMHHSFHTLNQTLMDMFEKCDHDQQQYELVYQDKEGDWLLAQDISW