AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene030632

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene030632.t1 MTR_8g093500 93.361 241 14 1 1 239 21 261 9.43e-145 405
MS.gene030632.t1 MTR_3g101810 73.958 96 25 0 60 155 139 234 5.78e-47 157
MS.gene030632.t1 MTR_5g017210 63.636 110 40 0 60 169 105 214 6.47e-37 130
MS.gene030632.t1 MTR_8g015450 60.577 104 36 2 58 156 289 392 8.05e-29 112
MS.gene030632.t1 MTR_2g100490 62.105 95 35 1 63 156 260 354 8.11e-27 107
MS.gene030632.t1 MTR_7g069590 67.857 56 18 0 98 153 32 87 1.28e-20 85.5
MS.gene030632.t1 MTR_5g079500 44.444 99 53 1 58 154 182 280 6.85e-20 87.0
MS.gene030632.t1 MTR_5g005110 58.108 74 30 1 84 156 215 288 1.51e-19 86.3
MS.gene030632.t1 MTR_1g106460 41.176 102 59 1 56 156 201 302 6.92e-19 84.3
MS.gene030632.t1 MTR_1g018090 66.071 56 19 0 101 156 283 338 7.30e-19 84.7
MS.gene030632.t1 MTR_1g106470 66.071 56 19 0 101 156 205 260 2.56e-18 82.4
MS.gene030632.t1 MTR_3g103030 60.606 66 25 1 92 156 228 293 6.51e-18 81.6
MS.gene030632.t1 MTR_4g131160 50.667 75 37 0 80 154 184 258 1.93e-15 75.1
MS.gene030632.t1 MTR_4g131160 50.667 75 37 0 80 154 187 261 1.99e-15 75.1
MS.gene030632.t1 MTR_1g106480 54.237 59 27 0 96 154 73 131 8.62e-15 70.1
MS.gene030632.t1 MTR_2g067000 46.053 76 39 1 82 155 145 220 4.72e-14 70.5
MS.gene030632.t1 MTR_1g080890 50.000 70 35 0 85 154 186 255 1.02e-13 70.1
MS.gene030632.t1 MTR_1g060700 59.259 54 22 0 102 155 357 410 2.71e-13 68.9
MS.gene030632.t1 MTR_2g089070 52.632 57 27 0 102 158 146 202 2.92e-13 68.2
MS.gene030632.t1 MTR_4g033295 57.143 56 23 1 102 156 128 183 1.04e-11 62.4
MS.gene030632.t1 MTR_4g033295 59.259 54 21 1 102 154 128 181 2.62e-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.gene030632.t1 AT5G09750 80.734 109 14 1 65 166 92 200 6.78e-46 153
MS.gene030632.t1 AT4G00120 80.899 89 17 0 67 155 87 175 1.18e-45 151
MS.gene030632.t1 AT3G21330 52.632 133 56 1 56 188 233 358 9.58e-38 135
MS.gene030632.t1 AT5G67060 76.923 91 21 0 65 155 83 173 9.13e-37 129
MS.gene030632.t1 AT5G67060 76.923 91 21 0 65 155 95 185 1.40e-36 129
MS.gene030632.t1 AT3G50330 74.725 91 23 0 65 155 92 182 2.48e-35 125
MS.gene030632.t1 AT5G01305 64.179 67 24 0 90 156 35 101 3.63e-21 87.4
MS.gene030632.t1 AT2G14760 67.857 56 18 0 101 156 246 301 5.99e-19 84.7
MS.gene030632.t1 AT4G33880 67.857 56 18 0 101 156 275 330 6.82e-19 84.7
MS.gene030632.t1 AT5G43175 47.500 80 42 0 77 156 117 196 6.99e-19 82.8
MS.gene030632.t1 AT5G37800 54.167 72 25 1 83 154 200 263 3.46e-18 82.0
MS.gene030632.t1 AT1G27740 50.704 71 35 0 86 156 161 231 1.02e-17 80.1
MS.gene030632.t1 AT1G66470 64.815 54 19 0 101 154 204 257 1.40e-17 80.5
MS.gene030632.t1 AT4G30980 59.091 66 26 1 90 154 127 192 1.94e-16 77.4
MS.gene030632.t1 AT4G30980 59.091 66 26 1 90 154 175 240 3.79e-16 77.0
MS.gene030632.t1 AT2G24260 62.963 54 20 0 101 154 44 97 4.51e-16 75.5
MS.gene030632.t1 AT2G24260 62.963 54 20 0 101 154 147 200 1.23e-15 75.5
MS.gene030632.t1 AT2G14760 55.072 69 18 1 101 156 246 314 1.39e-15 75.1
MS.gene030632.t1 AT5G58010 52.113 71 33 1 85 154 91 161 5.93e-15 73.2

Find 53 sgRNAs with CRISPR-Local

Find 58 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CTATGAATTCTTCTGGAATT+TGG 0.166878 4.2:+9230433 MS.gene030632:CDS
CATAGAAGCTGTATCCATTT+TGG 0.181268 4.2:-9230763 None:intergenic
GGTTCACTCAGTGACATATT+AGG 0.250977 4.2:+9230507 MS.gene030632:CDS
TTGTTATTGTCTCCTTCTTC+TGG 0.266342 4.2:+9230924 MS.gene030632:CDS
CAAGTTCCTATGAATTCTTC+TGG 0.298023 4.2:+9230426 MS.gene030632:CDS
ATCATGCTGTTGTAGCTATT+TGG 0.316175 4.2:-9230459 None:intergenic
CTTCTTCTGGTTGTGACGTC+TGG 0.336110 4.2:+9230937 MS.gene030632:CDS
GTGGAAGTGAGTAGTAAATT+TGG 0.351622 4.2:-9230969 None:intergenic
ATTCGAACGTTTCTTCGCTT+TGG 0.353088 4.2:-9230648 None:intergenic
TGTTCCTGGTGGAACCAAAA+TGG 0.358384 4.2:+9230749 MS.gene030632:CDS
TGTCTAGCTGCAACACTTTG+TGG 0.381712 4.2:-9230681 None:intergenic
ATCCTTCAAAGACTTGTTCC+TGG 0.399593 4.2:+9230735 MS.gene030632:CDS
GAAGAACAAGAAGAAGAGTT+AGG 0.401481 4.2:+9230552 MS.gene030632:CDS
AGAAGAGTTAGGAGCTATGA+AGG 0.405429 4.2:+9230563 MS.gene030632:CDS
GTTCACTCAGTGACATATTA+GGG 0.414540 4.2:+9230508 MS.gene030632:CDS
GATCTTGTTGGAGAATAATA+CGG 0.432514 4.2:-9230398 None:intergenic
AGTAGTAAATTTGGTGCAAA+AGG 0.442540 4.2:-9230960 None:intergenic
GTTCTTCTACATCTTCGATT+CGG 0.446833 4.2:-9230536 None:intergenic
TCCGGCGTCAAATTGAATTC+CGG 0.450878 4.2:-9231018 None:intergenic
CAAATTCCAGAAGAATTCAT+AGG 0.451806 4.2:-9230432 None:intergenic
CAGAAGAATTCATAGGAACT+TGG 0.471897 4.2:-9230425 None:intergenic
CACCAGGAACAAGTCTTTGA+AGG 0.481487 4.2:-9230737 None:intergenic
GAACTTGGTGGTGATCTTGT+TGG 0.483925 4.2:-9230410 None:intergenic
CTTCTACATCTTCGATTCGG+TGG 0.493447 4.2:-9230533 None:intergenic
CAAGATTGCAGCTATGCAAC+CGG 0.495861 4.2:+9230596 MS.gene030632:CDS
GCACCACCACCACCTTCATC+AGG 0.499844 4.2:+9230486 MS.gene030632:CDS
GTCCACTGTGGCAGCTGTTG+TGG 0.509617 4.2:-9230988 None:intergenic
CAGACGTCACAACCAGAAGA+AGG 0.532660 4.2:-9230936 None:intergenic
TAGCTACAACAGCATGATCA+TGG 0.539866 4.2:+9230464 MS.gene030632:CDS
ATGCTGTTGTAGCTATTTGG+TGG 0.542016 4.2:-9230456 None:intergenic
GAACCTGATGAAGGTGGTGG+TGG 0.552409 4.2:-9230489 None:intergenic
ATGAACATGTGAATGTCCTC+CGG 0.556908 4.2:-9231036 None:intergenic
GGCGTCAAATTGAATTCCGG+TGG 0.574382 4.2:-9231015 None:intergenic
CAAGAACTTAACATAACGAA+TGG 0.583966 4.2:-9230796 None:intergenic
TCACATGTTCATGCTTGTGA+AGG 0.591006 4.2:+9231047 MS.gene030632:CDS
GCCACAGTGGACTTACCCAC+CGG 0.591865 4.2:+9230999 MS.gene030632:CDS
AAGAATTCATAGGAACTTGG+TGG 0.592411 4.2:-9230422 None:intergenic
ACTCACTAATTACCTCATGA+TGG 0.592814 4.2:-9231085 None:intergenic
GACAATAACAAAGCACTAGG+AGG 0.606861 4.2:-9230912 None:intergenic
GGAGACAATAACAAAGCACT+AGG 0.609214 4.2:-9230915 None:intergenic
GGAATTCAATTTGACGCCGG+AGG 0.622262 4.2:+9231020 MS.gene030632:CDS
GCTGCTGGGTCGATATCCAC+CGG 0.627073 4.2:-9230615 None:intergenic
CTTCAAAGACTTGTTCCTGG+TGG 0.627271 4.2:+9230738 MS.gene030632:CDS
ACCGGAATTCAATTTGACGC+CGG 0.643580 4.2:+9231017 MS.gene030632:CDS
ATCAAGCTTTAACCATCATG+AGG 0.658321 4.2:+9231073 MS.gene030632:CDS
TTAATGCATTGTGATGAAAG+TGG 0.662271 4.2:-9230882 None:intergenic
TCACTGAGTGAACCTGATGA+AGG 0.669394 4.2:-9230498 None:intergenic
GATTGCAGCTATGCAACCGG+TGG 0.671341 4.2:+9230599 MS.gene030632:CDS
GCGTCAAATTGAATTCCGGT+GGG 0.674022 4.2:-9231014 None:intergenic
TTCCACAACAGCTGCCACAG+TGG 0.676021 4.2:+9230986 MS.gene030632:CDS
AGTGAACCTGATGAAGGTGG+TGG 0.679836 4.2:-9230492 None:intergenic
CTGAGTGAACCTGATGAAGG+TGG 0.711599 4.2:-9230495 None:intergenic
TCCGGTGGGTAAGTCCACTG+TGG 0.759981 4.2:-9231000 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
CAAATTCCAGAAGAATTCAT+AGG - chr4.2:9230435-9230454 None:intergenic 30.0%
CAAGAACTTAACATAACGAA+TGG - chr4.2:9230799-9230818 None:intergenic 30.0%
GATCTTGTTGGAGAATAATA+CGG - chr4.2:9230401-9230420 None:intergenic 30.0%
TTAATGCATTGTGATGAAAG+TGG - chr4.2:9230885-9230904 None:intergenic 30.0%
!! AGTAGTAAATTTGGTGCAAA+AGG - chr4.2:9230963-9230982 None:intergenic 30.0%
!! CTATGAATTCTTCTGGAATT+TGG + chr4.2:9230433-9230452 MS.gene030632:CDS 30.0%
!!! TGTTGTTGTTGTTGATTTTG+AGG - chr4.2:9230852-9230871 None:intergenic 30.0%
AAGAATTCATAGGAACTTGG+TGG - chr4.2:9230425-9230444 None:intergenic 35.0%
ACTCACTAATTACCTCATGA+TGG - chr4.2:9231088-9231107 None:intergenic 35.0%
ATCATGCTGTTGTAGCTATT+TGG - chr4.2:9230462-9230481 None:intergenic 35.0%
CAAGTTCCTATGAATTCTTC+TGG + chr4.2:9230426-9230445 MS.gene030632:CDS 35.0%
CAGAAGAATTCATAGGAACT+TGG - chr4.2:9230428-9230447 None:intergenic 35.0%
GAAGAACAAGAAGAAGAGTT+AGG + chr4.2:9230552-9230571 MS.gene030632:CDS 35.0%
GTGGAAGTGAGTAGTAAATT+TGG - chr4.2:9230972-9230991 None:intergenic 35.0%
GTTCACTCAGTGACATATTA+GGG + chr4.2:9230508-9230527 MS.gene030632:CDS 35.0%
GTTCTTCTACATCTTCGATT+CGG - chr4.2:9230539-9230558 None:intergenic 35.0%
! ATCAAGCTTTAACCATCATG+AGG + chr4.2:9231073-9231092 MS.gene030632:CDS 35.0%
! CATAGAAGCTGTATCCATTT+TGG - chr4.2:9230766-9230785 None:intergenic 35.0%
! TTGTTATTGTCTCCTTCTTC+TGG + chr4.2:9230924-9230943 MS.gene030632:CDS 35.0%
!!! TTGTTGTTGATTTTGAGGAG+TGG - chr4.2:9230847-9230866 None:intergenic 35.0%
AGAAGAGTTAGGAGCTATGA+AGG + chr4.2:9230563-9230582 MS.gene030632:CDS 40.0%
ATGAACATGTGAATGTCCTC+CGG - chr4.2:9231039-9231058 None:intergenic 40.0%
ATGCTGTTGTAGCTATTTGG+TGG - chr4.2:9230459-9230478 None:intergenic 40.0%
ATTCGAACGTTTCTTCGCTT+TGG - chr4.2:9230651-9230670 None:intergenic 40.0%
GGTTCACTCAGTGACATATT+AGG + chr4.2:9230507-9230526 MS.gene030632:CDS 40.0%
TAGCTACAACAGCATGATCA+TGG + chr4.2:9230464-9230483 MS.gene030632:CDS 40.0%
TCACATGTTCATGCTTGTGA+AGG + chr4.2:9231047-9231066 MS.gene030632:CDS 40.0%
! ATCCTTCAAAGACTTGTTCC+TGG + chr4.2:9230735-9230754 MS.gene030632:CDS 40.0%
! GACAATAACAAAGCACTAGG+AGG - chr4.2:9230915-9230934 None:intergenic 40.0%
! GGAGACAATAACAAAGCACT+AGG - chr4.2:9230918-9230937 None:intergenic 40.0%
ACCGGAATTCAATTTGACGC+CGG + chr4.2:9231017-9231036 MS.gene030632:CDS 45.0%
CAAGATTGCAGCTATGCAAC+CGG + chr4.2:9230596-9230615 MS.gene030632:CDS 45.0%
CACCAGGAACAAGTCTTTGA+AGG - chr4.2:9230740-9230759 None:intergenic 45.0%
GCGTCAAATTGAATTCCGGT+GGG - chr4.2:9231017-9231036 None:intergenic 45.0%
TCACTGAGTGAACCTGATGA+AGG - chr4.2:9230501-9230520 None:intergenic 45.0%
TCCGGCGTCAAATTGAATTC+CGG - chr4.2:9231021-9231040 None:intergenic 45.0%
TGTCTAGCTGCAACACTTTG+TGG - chr4.2:9230684-9230703 None:intergenic 45.0%
TGTTCCTGGTGGAACCAAAA+TGG + chr4.2:9230749-9230768 MS.gene030632:CDS 45.0%
! CTTCAAAGACTTGTTCCTGG+TGG + chr4.2:9230738-9230757 MS.gene030632:CDS 45.0%
!! CTTCTACATCTTCGATTCGG+TGG - chr4.2:9230536-9230555 None:intergenic 45.0%
!! GAACTTGGTGGTGATCTTGT+TGG - chr4.2:9230413-9230432 None:intergenic 45.0%
!! TTGGTTTTCGAATCGCTGCT+GGG - chr4.2:9230632-9230651 None:intergenic 45.0%
!!! GTATCCATTTTGGTTCCACC+AGG - chr4.2:9230756-9230775 None:intergenic 45.0%
!!! TTTGGTTTTCGAATCGCTGC+TGG - chr4.2:9230633-9230652 None:intergenic 45.0%
AGTGAACCTGATGAAGGTGG+TGG - chr4.2:9230495-9230514 None:intergenic 50.0%
CAGACGTCACAACCAGAAGA+AGG - chr4.2:9230939-9230958 None:intergenic 50.0%
CTGAGTGAACCTGATGAAGG+TGG - chr4.2:9230498-9230517 None:intergenic 50.0%
GGAATTCAATTTGACGCCGG+AGG + chr4.2:9231020-9231039 MS.gene030632:CDS 50.0%
GGCGTCAAATTGAATTCCGG+TGG - chr4.2:9231018-9231037 None:intergenic 50.0%
! CTTCTTCTGGTTGTGACGTC+TGG + chr4.2:9230937-9230956 MS.gene030632:CDS 50.0%
GATTGCAGCTATGCAACCGG+TGG + chr4.2:9230599-9230618 MS.gene030632:CDS 55.0%
TTCCACAACAGCTGCCACAG+TGG + chr4.2:9230986-9231005 MS.gene030632:CDS 55.0%
! GAACCTGATGAAGGTGGTGG+TGG - chr4.2:9230492-9230511 None:intergenic 55.0%
GCACCACCACCACCTTCATC+AGG + chr4.2:9230486-9230505 MS.gene030632:CDS 60.0%
GCTGCTGGGTCGATATCCAC+CGG - chr4.2:9230618-9230637 None:intergenic 60.0%
GTCCACTGTGGCAGCTGTTG+TGG - chr4.2:9230991-9231010 None:intergenic 60.0%
TCCGGTGGGTAAGTCCACTG+TGG - chr4.2:9231003-9231022 None:intergenic 60.0%
! GCCACAGTGGACTTACCCAC+CGG + chr4.2:9230999-9231018 MS.gene030632:CDS 60.0%


Chromosome Type Strat End Strand Name
chr4.2 gene 9230378 9231109 9230378 ID=MS.gene030632
chr4.2 mRNA 9230378 9231109 9230378 ID=MS.gene030632.t1;Parent=MS.gene030632
chr4.2 exon 9230378 9231109 9230378 ID=MS.gene030632.t1.exon1;Parent=MS.gene030632.t1
chr4.2 CDS 9230378 9231109 9230378 ID=cds.MS.gene030632.t1;Parent=MS.gene030632.t1
Gene Sequence

>MS.gene030632

ATGGAAACAAATGAACAAAACCGTATTATTCTCCAACAAGATCACCACCAAGTTCCTATGAATTCTTCTGGAATTTGGCCACCAAATAGCTACAACAGCATGATCATGGCACCACCACCACCTTCATCAGGTTCACTCAGTGACATATTAGGGATCCACCGAATCGAAGATGTAGAAGAACAAGAAGAAGAGTTAGGAGCTATGAAGGAAATGATGTACAAGATTGCAGCTATGCAACCGGTGGATATCGACCCAGCAGCGATTCGAAAACCAAAGCGAAGAAACGTTCGAATCAGCGACGATCCACAAAGTGTTGCAGCTAGACATAGAAGAGAAAGAATCAGTGAGAAGATTCGTATCCTTCAAAGACTTGTTCCTGGTGGAACCAAAATGGATACAGCTTCTATGCTTGATGAAGCCATTCGTTATGTTAAGTTCTTGAAGAGACAAATCAAGTTGCTTCAATCCACTCCTCAAAATCAACAACAACAACACATTCAATTGCCACTTTCATCACAATGCATTAATTCTACTCCTCCTAGTGCTTTGTTATTGTCTCCTTCTTCTGGTTGTGACGTCTGGCCTTTTGCACCAAATTTACTACTCACTTCCACAACAGCTGCCACAGTGGACTTACCCACCGGAATTCAATTTGACGCCGGAGGACATTCACATGTTCATGCTTGTGAAGGCTCATCAAGCTTTAACCATCATGAGGTAATTAGTGAGTGA
Protein sequence

>MS.gene030632.t1

METNEQNRIILQQDHHQVPMNSSGIWPPNSYNSMIMAPPPPSSGSLSDILGIHRIEDVEEQEEELGAMKEMMYKIAAMQPVDIDPAAIRKPKRRNVRISDDPQSVAARHRRERISEKIRILQRLVPGGTKMDTASMLDEAIRYVKFLKRQIKLLQSTPQNQQQQHIQLPLSSQCINSTPPSALLLSPSSGCDVWPFAPNLLLTSTTAATVDLPTGIQFDAGGHSHVHACEGSSSFNHHEVISE