AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene70229

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene70229.t1 MTR_8g093500 92.946 241 15 1 1 239 21 261 4.09e-144 404
MS.gene70229.t1 MTR_3g101810 73.958 96 25 0 60 155 139 234 5.08e-47 157
MS.gene70229.t1 MTR_5g017210 64.545 110 39 0 60 169 105 214 1.13e-37 132
MS.gene70229.t1 MTR_8g015450 60.577 104 36 2 58 156 289 392 6.06e-29 113
MS.gene70229.t1 MTR_2g100490 62.105 95 35 1 63 156 260 354 8.28e-27 107
MS.gene70229.t1 MTR_7g069590 67.857 56 18 0 98 153 32 87 1.23e-20 85.5
MS.gene70229.t1 MTR_5g079500 45.455 99 52 2 58 154 182 280 1.75e-19 85.9
MS.gene70229.t1 MTR_1g106460 41.176 102 59 1 56 156 201 302 6.39e-19 84.3
MS.gene70229.t1 MTR_1g018090 66.071 56 19 0 101 156 283 338 7.44e-19 84.7
MS.gene70229.t1 MTR_5g005110 66.071 56 19 0 101 156 233 288 8.28e-19 84.3
MS.gene70229.t1 MTR_1g106470 66.071 56 19 0 101 156 205 260 2.78e-18 82.0
MS.gene70229.t1 MTR_3g103030 60.606 66 25 1 92 156 228 293 6.51e-18 81.6
MS.gene70229.t1 MTR_4g131160 50.667 75 37 0 80 154 184 258 1.81e-15 75.1
MS.gene70229.t1 MTR_4g131160 50.667 75 37 0 80 154 187 261 1.92e-15 75.1
MS.gene70229.t1 MTR_1g106480 54.237 59 27 0 96 154 73 131 9.95e-15 69.7
MS.gene70229.t1 MTR_1g080890 50.000 70 35 0 85 154 186 255 1.73e-13 69.3
MS.gene70229.t1 MTR_2g067000 58.491 53 22 0 103 155 168 220 2.08e-13 68.6
MS.gene70229.t1 MTR_1g060700 59.259 54 22 0 102 155 357 410 2.51e-13 69.3
MS.gene70229.t1 MTR_2g089070 52.632 57 27 0 102 158 146 202 2.79e-13 68.2
MS.gene70229.t1 MTR_4g033295 57.143 56 23 1 102 156 128 183 1.07e-11 62.4
MS.gene70229.t1 MTR_4g033295 59.259 54 21 1 102 154 128 181 2.86e-11 61.2
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene70229.t1 AT5G09750 81.651 109 13 1 65 166 92 200 1.18e-46 155
MS.gene70229.t1 AT4G00120 82.022 89 16 0 67 155 87 175 1.92e-46 153
MS.gene70229.t1 AT3G21330 52.632 133 56 1 56 188 233 358 7.60e-38 136
MS.gene70229.t1 AT5G67060 75.824 91 22 0 65 155 83 173 3.79e-36 128
MS.gene70229.t1 AT5G67060 75.824 91 22 0 65 155 95 185 6.38e-36 127
MS.gene70229.t1 AT3G50330 74.725 91 23 0 65 155 92 182 2.09e-35 126
MS.gene70229.t1 AT5G01305 64.179 67 24 0 90 156 35 101 3.59e-21 87.4
MS.gene70229.t1 AT2G14760 67.857 56 18 0 101 156 246 301 6.36e-19 84.3
MS.gene70229.t1 AT5G43175 47.500 80 42 0 77 156 117 196 6.64e-19 82.8
MS.gene70229.t1 AT4G33880 67.857 56 18 0 101 156 275 330 7.09e-19 84.7
MS.gene70229.t1 AT1G27740 50.704 71 35 0 86 156 161 231 1.14e-17 80.1
MS.gene70229.t1 AT1G66470 64.815 54 19 0 101 154 204 257 1.56e-17 80.1
MS.gene70229.t1 AT5G37800 52.778 72 26 1 83 154 200 263 1.73e-17 80.1
MS.gene70229.t1 AT4G30980 59.091 66 26 1 90 154 127 192 2.08e-16 77.4
MS.gene70229.t1 AT4G30980 59.091 66 26 1 90 154 175 240 3.82e-16 77.0
MS.gene70229.t1 AT2G24260 62.963 54 20 0 101 154 44 97 4.24e-16 75.5
MS.gene70229.t1 AT2G24260 49.333 75 32 1 86 154 126 200 9.62e-16 75.9
MS.gene70229.t1 AT2G14760 55.072 69 18 1 101 156 246 314 1.43e-15 75.1
MS.gene70229.t1 AT5G58010 52.113 71 33 1 85 154 91 161 5.54e-15 73.2

Find 52 sgRNAs with CRISPR-Local

Find 57 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CTGTGAATTCTTCTGGAATT+TGG 0.193418 4.1:-8491272 MS.gene70229:CDS
CAAGTTCCTGTGAATTCTTC+TGG 0.235435 4.1:-8491279 MS.gene70229:CDS
GGTTCACTCAGTGACATATT+AGG 0.250977 4.1:-8491198 MS.gene70229:CDS
TTGTTATTGTCTCCTTCTTC+TGG 0.266342 4.1:-8490781 MS.gene70229:CDS
TGTTCCTGGTGGAACTAAAA+TGG 0.289003 4.1:-8490956 MS.gene70229:CDS
ATCATGCTGTTGTAGCTATT+TGG 0.316175 4.1:+8491246 None:intergenic
CTTCTTCTGGTTGTGACGTC+TGG 0.336110 4.1:-8490768 MS.gene70229:CDS
GTGGAAGTGAGTAGTAAATT+TGG 0.351622 4.1:+8490736 None:intergenic
ATTCGAACGTTTCTTCGCTT+TGG 0.353088 4.1:+8491057 None:intergenic
TGTCTAGCTGCAACACTTTG+TGG 0.381712 4.1:+8491024 None:intergenic
TCCGGCTTCAAATTGAATTC+CGG 0.385158 4.1:+8490687 None:intergenic
ATCCTTCAAAGACTTGTTCC+TGG 0.399593 4.1:-8490970 MS.gene70229:CDS
GAAGAACAAGAAGAAGAGTT+AGG 0.401481 4.1:-8491153 MS.gene70229:CDS
AGAAGAGTTAGGAGCTATGA+AGG 0.405429 4.1:-8491142 MS.gene70229:CDS
GTTCACTCAGTGACATATTA+GGG 0.414540 4.1:-8491197 MS.gene70229:CDS
GATCTTGTTGGAGAATAATA+CGG 0.432514 4.1:+8491307 None:intergenic
AGTAGTAAATTTGGTGCAAA+AGG 0.442540 4.1:+8490745 None:intergenic
CAGAAGAATTCACAGGAACT+TGG 0.442991 4.1:+8491280 None:intergenic
GTTCTTCTACATCTTCGATT+CGG 0.446833 4.1:+8491169 None:intergenic
CACCAGGAACAAGTCTTTGA+AGG 0.481487 4.1:+8490968 None:intergenic
CTTCTACATCTTCGATTCGG+TGG 0.493447 4.1:+8491172 None:intergenic
CAAGATTGCAGCTATGCAAC+CGG 0.495861 4.1:-8491109 MS.gene70229:CDS
GCACCACCACCACCTTCATC+AGG 0.499844 4.1:-8491219 MS.gene70229:CDS
GAACTTGGTGGTGATCTTGT+TGG 0.501628 4.1:+8491295 None:intergenic
GTCCACTGTGGCAGCTGTTG+TGG 0.509617 4.1:+8490717 None:intergenic
CAGACGTCACAACCAGAAGA+AGG 0.532660 4.1:+8490769 None:intergenic
GGCTTCAAATTGAATTCCGG+TGG 0.534628 4.1:+8490690 None:intergenic
ACCGGAATTCAATTTGAAGC+CGG 0.537068 4.1:-8490688 MS.gene70229:CDS
TAGCTACAACAGCATGATCA+TGG 0.539866 4.1:-8491241 MS.gene70229:CDS
ATGCTGTTGTAGCTATTTGG+TGG 0.542016 4.1:+8491249 None:intergenic
GAACCTGATGAAGGTGGTGG+TGG 0.552409 4.1:+8491216 None:intergenic
ATGAACATGTGAATGTCCTC+CGG 0.558161 4.1:+8490669 None:intergenic
CAAGAACTTAACATAACGAA+TGG 0.583966 4.1:+8490909 None:intergenic
AAGAATTCACAGGAACTTGG+TGG 0.585588 4.1:+8491283 None:intergenic
TCACATGTTCATGCTTGTGA+AGG 0.591006 4.1:-8490658 MS.gene70229:CDS
GCCACAGTGGACTTACCCAC+CGG 0.591865 4.1:-8490706 MS.gene70229:CDS
ACTCACTAATTACCTCATGA+TGG 0.592814 4.1:+8490620 None:intergenic
CAAATTCCAGAAGAATTCAC+AGG 0.600629 4.1:+8491273 None:intergenic
GACAATAACAAAGCACTAGG+AGG 0.606861 4.1:+8490793 None:intergenic
GGAATTCAATTTGAAGCCGG+AGG 0.608842 4.1:-8490685 MS.gene70229:CDS
GGAGACAATAACAAAGCACT+AGG 0.609214 4.1:+8490790 None:intergenic
CTTCAAAGACTTGTTCCTGG+TGG 0.627271 4.1:-8490967 MS.gene70229:CDS
GTTGCTGGGTCGATATCCAC+CGG 0.629556 4.1:+8491090 None:intergenic
GCTTCAAATTGAATTCCGGT+GGG 0.653003 4.1:+8490691 None:intergenic
ATCAAGCTTTAACCATCATG+AGG 0.658321 4.1:-8490632 MS.gene70229:CDS
TTAATGCATTGTGATGAAAG+TGG 0.662271 4.1:+8490823 None:intergenic
TCACTGAGTGAACCTGATGA+AGG 0.669394 4.1:+8491207 None:intergenic
GATTGCAGCTATGCAACCGG+TGG 0.671341 4.1:-8491106 MS.gene70229:CDS
TTCCACAACAGCTGCCACAG+TGG 0.676021 4.1:-8490719 MS.gene70229:CDS
AGTGAACCTGATGAAGGTGG+TGG 0.679836 4.1:+8491213 None:intergenic
CTGAGTGAACCTGATGAAGG+TGG 0.711599 4.1:+8491210 None:intergenic
TCCGGTGGGTAAGTCCACTG+TGG 0.759981 4.1:+8490705 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
CAAGAACTTAACATAACGAA+TGG + chr4.1:8491039-8491058 None:intergenic 30.0%
GATCTTGTTGGAGAATAATA+CGG + chr4.1:8490641-8490660 None:intergenic 30.0%
TTAATGCATTGTGATGAAAG+TGG + chr4.1:8491125-8491144 None:intergenic 30.0%
!! AGTAGTAAATTTGGTGCAAA+AGG + chr4.1:8491203-8491222 None:intergenic 30.0%
!!! TGTTGTTGTTGTTGATTTTG+AGG + chr4.1:8491092-8491111 None:intergenic 30.0%
ACTCACTAATTACCTCATGA+TGG + chr4.1:8491328-8491347 None:intergenic 35.0%
ATCATGCTGTTGTAGCTATT+TGG + chr4.1:8490702-8490721 None:intergenic 35.0%
CAAATTCCAGAAGAATTCAC+AGG + chr4.1:8490675-8490694 None:intergenic 35.0%
GAAGAACAAGAAGAAGAGTT+AGG - chr4.1:8490792-8490811 MS.gene70229:CDS 35.0%
GTGGAAGTGAGTAGTAAATT+TGG + chr4.1:8491212-8491231 None:intergenic 35.0%
GTTCACTCAGTGACATATTA+GGG - chr4.1:8490748-8490767 MS.gene70229:CDS 35.0%
GTTCTTCTACATCTTCGATT+CGG + chr4.1:8490779-8490798 None:intergenic 35.0%
! ATCAAGCTTTAACCATCATG+AGG - chr4.1:8491313-8491332 MS.gene70229:CDS 35.0%
! TTGTTATTGTCTCCTTCTTC+TGG - chr4.1:8491164-8491183 MS.gene70229:CDS 35.0%
!! CTGTGAATTCTTCTGGAATT+TGG - chr4.1:8490673-8490692 MS.gene70229:CDS 35.0%
!!! TTGTTGTTGATTTTGAGGAG+TGG + chr4.1:8491087-8491106 None:intergenic 35.0%
AAGAATTCACAGGAACTTGG+TGG + chr4.1:8490665-8490684 None:intergenic 40.0%
AGAAGAGTTAGGAGCTATGA+AGG - chr4.1:8490803-8490822 MS.gene70229:CDS 40.0%
ATGAACATGTGAATGTCCTC+CGG + chr4.1:8491279-8491298 None:intergenic 40.0%
ATGCTGTTGTAGCTATTTGG+TGG + chr4.1:8490699-8490718 None:intergenic 40.0%
ATTCGAACGTTTCTTCGCTT+TGG + chr4.1:8490891-8490910 None:intergenic 40.0%
CAAGTTCCTGTGAATTCTTC+TGG - chr4.1:8490666-8490685 MS.gene70229:CDS 40.0%
CAGAAGAATTCACAGGAACT+TGG + chr4.1:8490668-8490687 None:intergenic 40.0%
GCTTCAAATTGAATTCCGGT+GGG + chr4.1:8491257-8491276 None:intergenic 40.0%
GGTTCACTCAGTGACATATT+AGG - chr4.1:8490747-8490766 MS.gene70229:CDS 40.0%
TAGCTACAACAGCATGATCA+TGG - chr4.1:8490704-8490723 MS.gene70229:CDS 40.0%
TCACATGTTCATGCTTGTGA+AGG - chr4.1:8491287-8491306 MS.gene70229:CDS 40.0%
TCCGGCTTCAAATTGAATTC+CGG + chr4.1:8491261-8491280 None:intergenic 40.0%
TGTTCCTGGTGGAACTAAAA+TGG - chr4.1:8490989-8491008 MS.gene70229:CDS 40.0%
! ACCGGAATTCAATTTGAAGC+CGG - chr4.1:8491257-8491276 MS.gene70229:CDS 40.0%
! ATCCTTCAAAGACTTGTTCC+TGG - chr4.1:8490975-8490994 MS.gene70229:CDS 40.0%
! GACAATAACAAAGCACTAGG+AGG + chr4.1:8491155-8491174 None:intergenic 40.0%
! GGAGACAATAACAAAGCACT+AGG + chr4.1:8491158-8491177 None:intergenic 40.0%
!! TTGGTTTTCGAATCGTTGCT+GGG + chr4.1:8490872-8490891 None:intergenic 40.0%
!!! GTATCCATTTTAGTTCCACC+AGG + chr4.1:8490996-8491015 None:intergenic 40.0%
!!! TTTGGTTTTCGAATCGTTGC+TGG + chr4.1:8490873-8490892 None:intergenic 40.0%
CAAGATTGCAGCTATGCAAC+CGG - chr4.1:8490836-8490855 MS.gene70229:CDS 45.0%
CACCAGGAACAAGTCTTTGA+AGG + chr4.1:8490980-8490999 None:intergenic 45.0%
GGCTTCAAATTGAATTCCGG+TGG + chr4.1:8491258-8491277 None:intergenic 45.0%
TCACTGAGTGAACCTGATGA+AGG + chr4.1:8490741-8490760 None:intergenic 45.0%
TGTCTAGCTGCAACACTTTG+TGG + chr4.1:8490924-8490943 None:intergenic 45.0%
! CTTCAAAGACTTGTTCCTGG+TGG - chr4.1:8490978-8490997 MS.gene70229:CDS 45.0%
! GGAATTCAATTTGAAGCCGG+AGG - chr4.1:8491260-8491279 MS.gene70229:CDS 45.0%
!! CTTCTACATCTTCGATTCGG+TGG + chr4.1:8490776-8490795 None:intergenic 45.0%
!! GAACTTGGTGGTGATCTTGT+TGG + chr4.1:8490653-8490672 None:intergenic 45.0%
AGTGAACCTGATGAAGGTGG+TGG + chr4.1:8490735-8490754 None:intergenic 50.0%
CAGACGTCACAACCAGAAGA+AGG + chr4.1:8491179-8491198 None:intergenic 50.0%
CTGAGTGAACCTGATGAAGG+TGG + chr4.1:8490738-8490757 None:intergenic 50.0%
! CTTCTTCTGGTTGTGACGTC+TGG - chr4.1:8491177-8491196 MS.gene70229:CDS 50.0%
GATTGCAGCTATGCAACCGG+TGG - chr4.1:8490839-8490858 MS.gene70229:CDS 55.0%
GTTGCTGGGTCGATATCCAC+CGG + chr4.1:8490858-8490877 None:intergenic 55.0%
TTCCACAACAGCTGCCACAG+TGG - chr4.1:8491226-8491245 MS.gene70229:CDS 55.0%
! GAACCTGATGAAGGTGGTGG+TGG + chr4.1:8490732-8490751 None:intergenic 55.0%
GCACCACCACCACCTTCATC+AGG - chr4.1:8490726-8490745 MS.gene70229:CDS 60.0%
GTCCACTGTGGCAGCTGTTG+TGG + chr4.1:8491231-8491250 None:intergenic 60.0%
TCCGGTGGGTAAGTCCACTG+TGG + chr4.1:8491243-8491262 None:intergenic 60.0%
! GCCACAGTGGACTTACCCAC+CGG - chr4.1:8491239-8491258 MS.gene70229:CDS 60.0%


Chromosome Type Strat End Strand Name
chr4.1 gene 8490618 8491349 8490618 ID=MS.gene70229
chr4.1 mRNA 8490618 8491349 8490618 ID=MS.gene70229.t1;Parent=MS.gene70229
chr4.1 exon 8490618 8491349 8490618 ID=MS.gene70229.t1.exon1;Parent=MS.gene70229.t1
chr4.1 CDS 8490618 8491349 8490618 ID=cds.MS.gene70229.t1;Parent=MS.gene70229.t1
Gene Sequence

>MS.gene70229

ATGGAAACAAATGAACAAAACCGTATTATTCTCCAACAAGATCACCACCAAGTTCCTGTGAATTCTTCTGGAATTTGGCCACCAAATAGCTACAACAGCATGATCATGGCACCACCACCACCTTCATCAGGTTCACTCAGTGACATATTAGGGATCCACCGAATCGAAGATGTAGAAGAACAAGAAGAAGAGTTAGGAGCTATGAAGGAAATGATGTACAAGATTGCAGCTATGCAACCGGTGGATATCGACCCAGCAACGATTCGAAAACCAAAGCGAAGAAACGTTCGAATCAGCGACGATCCACAAAGTGTTGCAGCTAGACATAGAAGAGAAAGAATCAGTGAGAAGATTCGTATCCTTCAAAGACTTGTTCCTGGTGGAACTAAAATGGATACAGCTTCTATGCTTGATGAAGCCATTCGTTATGTTAAGTTCTTGAAGAGACAAATCAAGTTGCTTCAATCCACTCCTCAAAATCAACAACAACAACACATTCAATTGCCACTTTCATCACAATGCATTAATTCTACTCCTCCTAGTGCTTTGTTATTGTCTCCTTCTTCTGGTTGTGACGTCTGGCCTTTTGCACCAAATTTACTACTCACTTCCACAACAGCTGCCACAGTGGACTTACCCACCGGAATTCAATTTGAAGCCGGAGGACATTCACATGTTCATGCTTGTGAAGGCTCATCAAGCTTTAACCATCATGAGGTAATTAGTGAGTGA
Protein sequence

>MS.gene70229.t1

METNEQNRIILQQDHHQVPVNSSGIWPPNSYNSMIMAPPPPSSGSLSDILGIHRIEDVEEQEEELGAMKEMMYKIAAMQPVDIDPATIRKPKRRNVRISDDPQSVAARHRRERISEKIRILQRLVPGGTKMDTASMLDEAIRYVKFLKRQIKLLQSTPQNQQQQHIQLPLSSQCINSTPPSALLLSPSSGCDVWPFAPNLLLTSTTAATVDLPTGIQFEAGGHSHVHACEGSSSFNHHEVISE