AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1337600

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1337600 MtrunA17_Chr4g0072791 97.087 206 4 1 1 204 1 206 1.88e-152 421
Msa1337600 MtrunA17_Chr4g0072781 57.246 138 54 2 68 204 40 173 4.51e-54 170
Msa1337600 MtrunA17_Chr2g0280311 47.518 141 66 5 68 204 29 165 1.63e-43 143
Msa1337600 MtrunA17_Chr2g0281271 44.828 145 76 3 61 204 3 144 2.34e-42 140
Msa1337600 MtrunA17_Chr2g0280331 48.227 141 63 6 68 204 31 165 5.81e-40 134
Msa1337600 MtrunA17_Chr2g0280291 46.377 138 70 3 68 204 301 435 1.02e-39 140
Msa1337600 MtrunA17_Chr2g0280291 44.275 131 68 2 68 198 28 153 9.20e-36 130
Msa1337600 MtrunA17_Chr4g0049151 46.715 137 69 2 68 204 32 164 6.17e-39 131
Msa1337600 MtrunA17_Chr2g0295371 44.928 138 70 3 68 204 32 164 1.76e-38 130
Msa1337600 MtrunA17_Chr4g0049191 39.877 163 90 4 45 204 2 159 1.63e-33 117
Msa1337600 MtrunA17_Chr2g0280351 42.254 142 75 5 68 204 29 168 5.19e-33 116
Msa1337600 MtrunA17_Chr2g0280281 42.953 149 73 4 62 204 16 158 7.71e-32 113
Msa1337600 MtrunA17_Chr2g0280321 41.135 141 73 7 68 204 29 163 1.60e-31 112
Msa1337600 MtrunA17_Chr1g0181941 35.749 207 116 8 5 203 10 207 2.98e-31 113
Msa1337600 MtrunA17_Chr2g0280301 48.113 106 48 4 100 204 36 135 6.77e-30 107
Msa1337600 MtrunA17_Chr2g0280341 41.606 137 69 7 73 204 207 337 4.75e-25 99.8
Msa1337600 MtrunA17_Chr2g0280341 37.069 116 64 6 68 179 29 139 1.33e-14 71.2
Msa1337600 MtrunA17_Chr8g0373921 35.915 142 89 2 64 204 32 172 9.64e-24 92.8
Msa1337600 MtrunA17_Chr5g0403201 31.655 139 93 1 68 204 47 185 2.99e-22 89.4
Msa1337600 MtrunA17_Chr5g0403191 32.609 92 57 3 118 204 12 103 1.71e-11 58.5
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1337600 AT4G25780.1 61.688 154 59 0 51 204 37 190 1.11e-76 228
Msa1337600 AT4G25790.1 56.522 138 55 2 68 204 77 210 1.64e-52 168
Msa1337600 AT5G57625.1 48.125 160 78 2 46 204 52 207 2.75e-50 162
Msa1337600 AT4G30320.1 48.980 147 69 3 59 204 20 161 1.44e-47 154
Msa1337600 AT4G31470.1 44.886 176 90 3 30 204 16 185 7.43e-46 150
Msa1337600 AT1G01310.1 49.635 137 65 1 68 204 87 219 2.75e-45 150
Msa1337600 AT4G33720.1 49.635 137 64 2 68 204 32 163 1.01e-40 136
Msa1337600 AT3G19690.1 43.038 158 81 4 51 204 9 161 6.75e-40 134
Msa1337600 AT5G02730.1 45.775 142 71 3 65 204 56 193 9.41e-39 132
Msa1337600 AT2G14610.1 43.066 137 71 3 68 204 32 161 2.79e-37 127
Msa1337600 AT3G09590.1 46.809 141 69 3 66 204 50 186 7.31e-37 127
Msa1337600 AT5G26130.1 44.526 137 73 2 68 204 33 166 8.11e-36 124
Msa1337600 AT2G14580.1 40.876 137 74 2 68 204 32 161 7.66e-35 121
Msa1337600 AT1G50050.2 39.456 147 86 1 58 204 19 162 1.83e-33 117
Msa1337600 AT4G33730.1 41.606 137 73 4 69 204 42 172 2.69e-33 117
Msa1337600 AT4G33710.1 40.876 137 78 2 68 204 33 166 1.32e-30 110
Msa1337600 AT1G50060.1 43.066 137 74 1 68 204 29 161 4.55e-30 108
Msa1337600 AT2G19990.1 41.304 138 75 3 68 204 44 176 6.00e-30 109
Msa1337600 AT1G50050.1 38.686 137 81 1 58 194 19 152 7.66e-29 107
Msa1337600 AT5G66590.1 34.266 143 91 3 64 204 44 185 5.14e-24 94.4
Msa1337600 AT4G07820.1 32.117 137 86 4 68 204 31 160 1.94e-18 79.0
Msa1337600 AT2G19980.1 36.667 150 67 10 65 204 34 165 8.43e-15 69.3

Find 44 sgRNAs with CRISPR-Local

Find 50 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CCTGAAGATGGTTTCAAATT+AGG 0.121429 tig0001526:-257780 Msa1337600:CDS
TCTTCTGTTGGCTTAAATAT+TGG 0.269698 tig0001526:+258006 None:intergenic
TATGATTAATTAAATTAATA+TGG 0.291226 tig0001526:+257510 None:intergenic
CATTGTCTGGTTTCTTCTGT+TGG 0.325866 tig0001526:+257994 None:intergenic
GAATGTTCCACTTTGCAATC+TGG 0.345438 tig0001526:+257807 None:intergenic
ATTAGGAGAGAATATATATT+GGG 0.348184 tig0001526:-257763 Msa1337600:CDS
CCTAATTTGAAACCATCTTC+AGG 0.349768 tig0001526:+257780 None:intergenic
TTGTATATGGTCTCATTGTC+TGG 0.352683 tig0001526:+257981 None:intergenic
CTGACTAATTCATGTGTATC+TGG 0.360625 tig0001526:-257669 Msa1337600:CDS
AATTAGGAGAGAATATATAT+TGG 0.371913 tig0001526:-257764 Msa1337600:CDS
AAGTATCAAAACAGCTTTGT+TGG 0.382310 tig0001526:-257959 Msa1337600:CDS
TAGGAGAAGAAGAAGAAGGC+TGG 0.387786 tig0001526:+258042 None:intergenic
CATCAATGGAAGTTCCCATT+TGG 0.423106 tig0001526:+257881 None:intergenic
TGGAAAAGTACTAGAAGAAT+TGG 0.425934 tig0001526:-257615 Msa1337600:CDS
CAACGGATGCTGTAAAAGCT+TGG 0.458076 tig0001526:-257719 Msa1337600:CDS
ATTTAGTAAGAGCATCCAAA+TGG 0.467344 tig0001526:-257896 Msa1337600:CDS
AGGAGAAGAAGAAGAAGGCT+GGG 0.469788 tig0001526:+258043 None:intergenic
AGCTGGTAATCCCACATCAA+TGG 0.480192 tig0001526:+257867 None:intergenic
AACGGATGCTGTAAAAGCTT+GGG 0.485815 tig0001526:-257718 Msa1337600:CDS
GAGAATATATATTGGGGTAG+TGG 0.490490 tig0001526:-257756 Msa1337600:CDS
TTGAACAATACGCAAGGTGG+TGG 0.491083 tig0001526:-257845 Msa1337600:CDS
ATTGGGGTAGTGGCTCTGAT+TGG 0.492371 tig0001526:-257746 Msa1337600:CDS
GCAAGAGTTGTGTGTGATGA+TGG 0.498907 tig0001526:-257588 Msa1337600:CDS
TCTCCAACATAATTACCAAC+AGG 0.506191 tig0001526:+257537 None:intergenic
AGAAGAAGAAGGCTGGGGAC+TGG 0.506704 tig0001526:+258049 None:intergenic
GATCCTGTTGGTAATTATGT+TGG 0.511947 tig0001526:-257540 Msa1337600:CDS
TGAGTAGGAGAAGAAGAAGA+AGG 0.528726 tig0001526:+258038 None:intergenic
ACCTTGCGTATTGTTCAAGC+TGG 0.537913 tig0001526:+257850 None:intergenic
TTTAGTAAGAGCATCCAAAT+GGG 0.554322 tig0001526:-257895 Msa1337600:CDS
AATGGGAACTTCCATTGATG+TGG 0.559795 tig0001526:-257878 Msa1337600:CDS
TATTGGCTATATATTTGAGT+AGG 0.566022 tig0001526:+258023 None:intergenic
CAAGGTGGTGGGCTAGTCAA+AGG 0.567063 tig0001526:-257833 Msa1337600:CDS
GGAGAAGAAGAAGAAGGCTG+GGG 0.585095 tig0001526:+258044 None:intergenic
ATGGGAACTTCCATTGATGT+GGG 0.586774 tig0001526:-257877 Msa1337600:CDS
ACAGCTTTGTTGGAACTGCA+TGG 0.590173 tig0001526:-257949 Msa1337600:CDS
TGAACAATACGCAAGGTGGT+GGG 0.616960 tig0001526:-257844 Msa1337600:CDS
GACATTATACTCAGATTGTG+TGG 0.618377 tig0001526:-257635 Msa1337600:CDS
TTAGGAGAGAATATATATTG+GGG 0.623586 tig0001526:-257762 Msa1337600:CDS
TGGCTCTGATTGGACACCAA+CGG 0.632245 tig0001526:-257736 Msa1337600:CDS
TGTGTATCTGGTCAAATGTG+TGG 0.656492 tig0001526:-257657 Msa1337600:CDS
ACCAGCTTGAACAATACGCA+AGG 0.661122 tig0001526:-257851 Msa1337600:CDS
ACTTGTAACTATGATCCTGT+TGG 0.661520 tig0001526:-257552 Msa1337600:CDS
AGCTTGAACAATACGCAAGG+TGG 0.696278 tig0001526:-257848 Msa1337600:CDS
AAGGAAACCAGATTGCAAAG+TGG 0.700454 tig0001526:-257814 Msa1337600:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AATTAGGAGAGAATATATAT+TGG - tig0001526:257876-257895 Msa1337600:CDS 20.0%
!! ATTAGGAGAGAATATATATT+GGG - tig0001526:257877-257896 Msa1337600:CDS 20.0%
!! TATTGGCTATATATTTGAGT+AGG + tig0001526:257620-257639 None:intergenic 25.0%
!!! CTGTTTTGATACTTTGTATA+TGG + tig0001526:257675-257694 None:intergenic 25.0%
! TTAGGAGAGAATATATATTG+GGG - tig0001526:257878-257897 Msa1337600:CDS 25.0%
!! TCTTCTGTTGGCTTAAATAT+TGG + tig0001526:257637-257656 None:intergenic 30.0%
! AAGTATCAAAACAGCTTTGT+TGG - tig0001526:257681-257700 Msa1337600:CDS 30.0%
!! ATTTAGTAAGAGCATCCAAA+TGG - tig0001526:257744-257763 Msa1337600:CDS 30.0%
!! TTTAGTAAGAGCATCCAAAT+GGG - tig0001526:257745-257764 Msa1337600:CDS 30.0%
!! TGGAAAAGTACTAGAAGAAT+TGG - tig0001526:258025-258044 Msa1337600:CDS 30.0%
TGACAAAAATGAAGAAGCAG+AGG + tig0001526:257547-257566 None:intergenic 35.0%
TTGTATATGGTCTCATTGTC+TGG + tig0001526:257662-257681 None:intergenic 35.0%
! GAACATTCTTTTCCTGAAGA+TGG - tig0001526:257848-257867 Msa1337600:CDS 35.0%
! CCTAATTTGAAACCATCTTC+AGG + tig0001526:257863-257882 None:intergenic 35.0%
CCTGAAGATGGTTTCAAATT+AGG - tig0001526:257860-257879 Msa1337600:CDS 35.0%
GAGAATATATATTGGGGTAG+TGG - tig0001526:257884-257903 Msa1337600:CDS 35.0%
CTGACTAATTCATGTGTATC+TGG - tig0001526:257971-257990 Msa1337600:CDS 35.0%
GACATTATACTCAGATTGTG+TGG - tig0001526:258005-258024 Msa1337600:CDS 35.0%
ACTTGTAACTATGATCCTGT+TGG - tig0001526:258088-258107 Msa1337600:CDS 35.0%
!! GATCCTGTTGGTAATTATGT+TGG - tig0001526:258100-258119 Msa1337600:CDS 35.0%
TCTCCAACATAATTACCAAC+AGG + tig0001526:258106-258125 None:intergenic 35.0%
CAAAAATGAAGAAGCAGAGG+AGG + tig0001526:257544-257563 None:intergenic 40.0%
! TGAGAGAGTTTTTGTGGTGA+AGG + tig0001526:257570-257589 None:intergenic 40.0%
! ACTGGTTGAGAGAGTTTTTG+TGG + tig0001526:257576-257595 None:intergenic 40.0%
TGAGTAGGAGAAGAAGAAGA+AGG + tig0001526:257605-257624 None:intergenic 40.0%
! CATTGTCTGGTTTCTTCTGT+TGG + tig0001526:257649-257668 None:intergenic 40.0%
CATCAATGGAAGTTCCCATT+TGG + tig0001526:257762-257781 None:intergenic 40.0%
AATGGGAACTTCCATTGATG+TGG - tig0001526:257762-257781 Msa1337600:CDS 40.0%
ATGGGAACTTCCATTGATGT+GGG - tig0001526:257763-257782 Msa1337600:CDS 40.0%
AAGGAAACCAGATTGCAAAG+TGG - tig0001526:257826-257845 Msa1337600:CDS 40.0%
GAATGTTCCACTTTGCAATC+TGG + tig0001526:257836-257855 None:intergenic 40.0%
AACGGATGCTGTAAAAGCTT+GGG - tig0001526:257922-257941 Msa1337600:CDS 40.0%
TGTGTATCTGGTCAAATGTG+TGG - tig0001526:257983-258002 Msa1337600:CDS 40.0%
AGGAGAAGAAGAAGAAGGCT+GGG + tig0001526:257600-257619 None:intergenic 45.0%
TAGGAGAAGAAGAAGAAGGC+TGG + tig0001526:257601-257620 None:intergenic 45.0%
!! ACAGCTTTGTTGGAACTGCA+TGG - tig0001526:257691-257710 Msa1337600:CDS 45.0%
AGCTGGTAATCCCACATCAA+TGG + tig0001526:257776-257795 None:intergenic 45.0%
ACCAGCTTGAACAATACGCA+AGG - tig0001526:257789-257808 Msa1337600:CDS 45.0%
ACCTTGCGTATTGTTCAAGC+TGG + tig0001526:257793-257812 None:intergenic 45.0%
AGCTTGAACAATACGCAAGG+TGG - tig0001526:257792-257811 Msa1337600:CDS 45.0%
TTGAACAATACGCAAGGTGG+TGG - tig0001526:257795-257814 Msa1337600:CDS 45.0%
TGAACAATACGCAAGGTGGT+GGG - tig0001526:257796-257815 Msa1337600:CDS 45.0%
! CAAGCTTTTACAGCATCCGT+TGG + tig0001526:257923-257942 None:intergenic 45.0%
CAACGGATGCTGTAAAAGCT+TGG - tig0001526:257921-257940 Msa1337600:CDS 45.0%
GCAAGAGTTGTGTGTGATGA+TGG - tig0001526:258052-258071 Msa1337600:CDS 45.0%
GGAGAAGAAGAAGAAGGCTG+GGG + tig0001526:257599-257618 None:intergenic 50.0%
!! ATTGGGGTAGTGGCTCTGAT+TGG - tig0001526:257894-257913 Msa1337600:CDS 50.0%
!! TGGCTCTGATTGGACACCAA+CGG - tig0001526:257904-257923 Msa1337600:CDS 50.0%
AGAAGAAGAAGGCTGGGGAC+TGG + tig0001526:257594-257613 None:intergenic 55.0%
!! CAAGGTGGTGGGCTAGTCAA+AGG - tig0001526:257807-257826 Msa1337600:CDS 55.0%
Chromosome Type Strat End Strand Name
tig0001526 gene 257524 258138 257524 ID=Msa1337600;Name=Msa1337600
tig0001526 mRNA 257524 258138 257524 ID=Msa1337600-mRNA-1;Parent=Msa1337600;Name=Msa1337600-mRNA-1;_AED=0.00;_eAED=0.00;_QI=0|-1|0|1|-1|1|1|0|204
tig0001526 exon 257524 258138 257524 ID=Msa1337600-mRNA-1:exon:1231;Parent=Msa1337600-mRNA-1
tig0001526 CDS 257524 258138 257524 ID=Msa1337600-mRNA-1:cds;Parent=Msa1337600-mRNA-1
Gene Sequence

>Msa1337600

ATGAAATCTCATTTGCTCCTCCTCTGCTTCTTCATTTTTGTCACCTTCACCACAAAAACTCTCTCAACCAGTCCCCAGCCTTCTTCTTCTTCTCCTACTCAAATATATAGCCAATATTTAAGCCAACAGAAGAAACCAGACAATGAGACCATATACAAAGTATCAAAACAGCTTTGTTGGAACTGCATGGCAGAGTCACTAGAGTTTTTGTTCAGACACAATTTAGTAAGAGCATCCAAATGGGAACTTCCATTGATGTGGGATTACCAGCTTGAACAATACGCAAGGTGGTGGGCTAGTCAAAGGAAACCAGATTGCAAAGTGGAACATTCTTTTCCTGAAGATGGTTTCAAATTAGGAGAGAATATATATTGGGGTAGTGGCTCTGATTGGACACCAACGGATGCTGTAAAAGCTTGGGCTGATGAAGAGAAATATTACACATATCTGACTAATTCATGTGTATCTGGTCAAATGTGTGGACATTATACTCAGATTGTGTGGAAAAGTACTAGAAGAATTGGTTGTGCAAGAGTTGTGTGTGATGATGGAGATGTGTTCATGACTTGTAACTATGATCCTGTTGGTAATTATGTTGGAGAACGACCATATTAA
Protein sequence

>Msa1337600

MKSHLLLLCFFIFVTFTTKTLSTSPQPSSSSPTQIYSQYLSQQKKPDNETIYKVSKQLCWNCMAESLEFLFRHNLVRASKWELPLMWDYQLEQYARWWASQRKPDCKVEHSFPEDGFKLGENIYWGSGSDWTPTDAVKAWADEEKYYTYLTNSCVSGQMCGHYTQIVWKSTRRIGCARVVCDDGDVFMTCNYDPVGNYVGERPY*