AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0878010

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0878010 MtrunA17_Chr2g0287651 42.640 197 108 1 29 220 63 259 1.06e-47 167
Msa0878010 MtrunA17_Chr1g0203051 29.384 211 136 5 1 198 31 241 1.17e-26 107
Msa0878010 MtrunA17_Chr5g0448761 36.957 184 108 4 44 220 63 245 9.73e-25 101
Msa0878010 MtrunA17_Chr7g0258861 30.636 173 115 2 44 212 13 184 3.53e-19 84.0
Msa0878010 MtrunA17_Chr2g0324011 30.435 161 106 2 44 200 13 171 2.27e-18 83.2
Msa0878010 MtrunA17_Chr1g0202341 33.511 188 113 6 40 220 50 232 7.39e-17 79.0
Msa0878010 MtrunA17_Chr3g0082121 29.048 210 142 4 1 203 1 210 7.94e-17 78.6
Msa0878010 MtrunA17_Chr6g0458391 37.719 114 67 3 44 154 94 206 1.67e-16 77.8
Msa0878010 MtrunA17_Chr6g0458391 36.923 130 74 4 44 166 228 356 7.71e-16 75.9
Msa0878010 MtrunA17_Chr5g0441581 31.461 178 111 4 44 220 35 202 4.06e-16 76.6
Msa0878010 MtrunA17_Chr7g0238821 35.185 108 64 2 45 148 1 106 1.11e-15 70.5
Msa0878010 MtrunA17_Chr6g0451441 32.515 163 101 4 44 203 90 246 5.63e-15 73.2
Msa0878010 MtrunA17_Chr8g0389811 30.252 119 78 1 34 147 77 195 3.61e-14 68.6
Msa0878010 MtrunA17_Chr2g0329421 35.514 107 67 2 39 143 25 131 4.19e-14 68.6
Msa0878010 MtrunA17_Chr1g0171741 30.400 125 75 2 42 158 134 254 5.19e-14 68.9
Msa0878010 MtrunA17_Chr4g0033611 35.000 100 63 2 44 141 79 178 1.29e-13 67.8
Msa0878010 MtrunA17_Chr7g0233911 40.385 104 56 3 44 142 37 139 1.44e-13 67.0
Msa0878010 MtrunA17_Chr2g0294841 28.780 205 131 7 9 200 14 216 3.14e-13 68.2
Msa0878010 MtrunA17_Chr1g0203721 31.515 165 106 6 44 202 66 229 6.21e-13 67.4
Msa0878010 MtrunA17_Chr2g0276841 30.114 176 112 6 44 209 73 247 2.52e-12 65.5
Msa0878010 MtrunA17_Chr5g0431001 27.485 171 110 4 44 200 64 234 3.41e-12 65.1
Msa0878010 MtrunA17_Chr2g0296781 28.090 178 122 5 45 220 1 174 1.31e-11 63.5
Msa0878010 MtrunA17_Chr8g0363841 28.415 183 122 6 44 220 20 199 2.99e-11 62.4
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0878010 AT4G38180.1 34.419 215 132 5 4 210 35 248 4.88e-26 105
Msa0878010 AT3G07500.1 36.184 152 83 6 16 157 3 150 6.32e-17 76.6
Msa0878010 AT3G59470.2 35.514 107 67 2 39 143 80 186 1.03e-13 68.6
Msa0878010 AT3G59470.3 35.514 107 67 2 39 143 68 174 1.05e-13 68.6
Msa0878010 AT3G59470.1 35.514 107 67 2 39 143 68 174 1.05e-13 68.6
Msa0878010 AT1G10240.2 29.143 175 115 5 44 209 51 225 5.39e-13 67.8
Msa0878010 AT1G10240.1 29.143 175 115 5 44 209 51 225 5.39e-13 67.8
Msa0878010 AT5G28530.1 26.966 178 122 4 44 214 58 234 6.46e-13 67.8
Msa0878010 AT5G28530.3 26.966 178 122 4 44 214 58 234 6.95e-13 67.4
Msa0878010 AT5G28530.2 26.966 178 122 4 44 214 58 234 6.95e-13 67.4
Msa0878010 AT5G28530.5 26.966 178 122 4 44 214 58 234 9.59e-13 67.0
Msa0878010 AT5G28530.4 26.966 178 122 4 44 214 58 234 9.79e-13 67.0
Msa0878010 AT4G12850.4 36.522 115 68 3 39 152 9 119 1.50e-12 63.2
Msa0878010 AT4G12850.2 38.235 102 61 2 39 139 9 109 2.24e-12 62.8
Msa0878010 AT4G12850.1 35.246 122 74 3 39 156 9 129 7.04e-12 62.4
Msa0878010 AT5G18960.2 39.175 97 47 3 44 139 46 131 1.40e-11 63.9
Msa0878010 AT5G18960.1 39.175 97 47 3 44 139 46 131 1.40e-11 63.9
Msa0878010 AT4G15090.1 28.962 183 121 6 44 220 54 233 4.98e-11 62.0
Msa0878010 AT4G15090.5 28.962 183 121 6 44 220 54 233 4.98e-11 62.0
Msa0878010 AT4G15090.3 28.962 183 121 6 44 220 54 233 4.98e-11 62.0
Msa0878010 AT4G15090.2 28.962 183 121 6 44 220 54 233 4.98e-11 62.0
Msa0878010 AT4G15090.4 28.962 183 121 6 44 220 54 233 4.98e-11 62.0

Find 49 sgRNAs with CRISPR-Local

Find 52 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ACTAATAAGTGGAGAGTTTC+TGG 0.119642 6_1:+18359764 Msa0878010:CDS
TGTTAGAACCTGTCATATTT+TGG 0.145212 6_1:+18359904 Msa0878010:CDS
TCACTCAATTGACGGTTCTT+AGG 0.285255 6_1:-18359842 None:intergenic
TGCTGCGTTGAGTTATTTGT+AGG 0.320569 6_1:+18360039 Msa0878010:CDS
TGAAGAAGGAAAAGAGGATA+TGG 0.353695 6_1:+18359460 Msa0878010:CDS
TGGATACTTACAAGAAGATT+AGG 0.354642 6_1:+18359480 Msa0878010:CDS
TCCAACCCGTTATGCTCATT+TGG 0.356553 6_1:+18359817 Msa0878010:CDS
GAAAGGAGGTCATGAGAGTC+TGG 0.365097 6_1:+18359943 Msa0878010:CDS
GAAGGAAAGGTAAGAATAGA+AGG 0.386587 6_1:+18360004 Msa0878010:CDS
GCAAACGATGGAGACATAAA+TGG 0.387588 6_1:+18359404 Msa0878010:CDS
TCTGATAAAGCCCTTGTTGA+TGG 0.437123 6_1:+18359866 Msa0878010:CDS
TATCAGATTCACTCAATTGA+CGG 0.439464 6_1:-18359850 None:intergenic
GGATACTTACAAGAAGATTA+GGG 0.465987 6_1:+18359481 Msa0878010:CDS
CAAGAAGATTAGGGAATTGA+CGG 0.467663 6_1:+18359490 Msa0878010:CDS
AGGAACCAAATGAGCATAAC+GGG 0.471013 6_1:-18359822 None:intergenic
ATTTATGTCTCCATCGTTTG+CGG 0.473976 6_1:-18359402 None:intergenic
AATGGTGTGTTTAATGAAGA+AGG 0.477078 6_1:+18359446 Msa0878010:CDS
GAAGATTTAGCCAGCGGTAA+TGG 0.477870 6_1:+18359428 Msa0878010:CDS
TAAATGTTGATACTAATAAG+TGG 0.482914 6_1:+18359753 Msa0878010:CDS
GGATGATGATATAAGAGGAT+TGG 0.496802 6_1:+18359511 Msa0878010:CDS
TTGACGGATGATGATATAAG+AGG 0.497315 6_1:+18359506 Msa0878010:CDS
GAAATCTATGCAGATTGTCA+TGG 0.498853 6_1:+18359569 Msa0878010:CDS
TATAACTACTTATACAATGA+AGG 0.501991 6_1:+18359986 Msa0878010:CDS
GATGTAAACAAAGATGATGA+TGG 0.508994 6_1:+18359611 Msa0878010:CDS
AGAAACAAAGTACATATTCG+AGG 0.529955 6_1:+18359687 Msa0878010:CDS
TGCAGATTGTCATGGGTTTG+TGG 0.531824 6_1:+18359577 Msa0878010:CDS
AAATCTATGCAGATTGTCAT+GGG 0.533515 6_1:+18359570 Msa0878010:CDS
ATTTAAATGGCCGCAAACGA+TGG 0.539363 6_1:+18359392 None:intergenic
TGCAGAACACTTAGTTCGAA+TGG 0.539821 6_1:-18359714 None:intergenic
GGAAAGGTAAGAATAGAAGG+TGG 0.544372 6_1:+18360007 Msa0878010:CDS
TAGGAACCAAATGAGCATAA+CGG 0.549503 6_1:-18359823 None:intergenic
CATAAAACCCAAAATATGAC+AGG 0.552239 6_1:-18359912 None:intergenic
ATTAAACACACCATTACCGC+TGG 0.561779 6_1:-18359438 None:intergenic
GTTTAATGAAGAAGGAAAAG+AGG 0.567512 6_1:+18359454 Msa0878010:CDS
AACGGGTTGGAGTTAACTCA+TGG 0.579913 6_1:-18359805 None:intergenic
CTACTTATACAATGAAGGAA+AGG 0.580957 6_1:+18359991 Msa0878010:CDS
ATGTAAACAAAGATGATGAT+GGG 0.584402 6_1:+18359612 Msa0878010:CDS
AGTTAACTCATGGTTGTGTG+AGG 0.591294 6_1:-18359795 None:intergenic
ACCAAATGAGCATAACGGGT+TGG 0.596668 6_1:-18359818 None:intergenic
TCGATTAGTATGTAATAGAG+AGG 0.600970 6_1:+18359649 Msa0878010:CDS
TTTATGATGGCTCAGAAAGG+AGG 0.609928 6_1:+18359929 Msa0878010:CDS
AAAGGAGGTCATGAGAGTCT+GGG 0.612373 6_1:+18359944 Msa0878010:CDS
GTGCATGAAGACCATCAACA+AGG 0.624046 6_1:-18359877 None:intergenic
GTTAACTCATGGTTGTGTGA+GGG 0.630795 6_1:-18359794 None:intergenic
CGATTAGTATGTAATAGAGA+GGG 0.642038 6_1:+18359650 Msa0878010:CDS
TTCGAACTAAGTGTTCTGCA+AGG 0.661356 6_1:+18359717 Msa0878010:CDS
TGCATGAAGACCATCAACAA+GGG 0.667132 6_1:-18359876 None:intergenic
AATGGTGAAGATTTAGCCAG+CGG 0.677055 6_1:+18359422 Msa0878010:CDS
GTTGATGGTCTTCATGCACA+CGG 0.677402 6_1:+18359881 Msa0878010:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TAAATGTTGATACTAATAAG+TGG + chr6_1:18359753-18359772 Msa0878010:CDS 20.0%
!! TATAACTACTTATACAATGA+AGG + chr6_1:18359986-18360005 Msa0878010:CDS 20.0%
! ATGTAAACAAAGATGATGAT+GGG + chr6_1:18359612-18359631 Msa0878010:CDS 25.0%
!!! TCATATTTTGGGTTTTATGA+TGG + chr6_1:18359916-18359935 Msa0878010:CDS 25.0%
AATGGTGTGTTTAATGAAGA+AGG + chr6_1:18359446-18359465 Msa0878010:CDS 30.0%
GTTTAATGAAGAAGGAAAAG+AGG + chr6_1:18359454-18359473 Msa0878010:CDS 30.0%
TGGATACTTACAAGAAGATT+AGG + chr6_1:18359480-18359499 Msa0878010:CDS 30.0%
GGATACTTACAAGAAGATTA+GGG + chr6_1:18359481-18359500 Msa0878010:CDS 30.0%
AAATCTATGCAGATTGTCAT+GGG + chr6_1:18359570-18359589 Msa0878010:CDS 30.0%
GATGTAAACAAAGATGATGA+TGG + chr6_1:18359611-18359630 Msa0878010:CDS 30.0%
TCGATTAGTATGTAATAGAG+AGG + chr6_1:18359649-18359668 Msa0878010:CDS 30.0%
CGATTAGTATGTAATAGAGA+GGG + chr6_1:18359650-18359669 Msa0878010:CDS 30.0%
AGAAACAAAGTACATATTCG+AGG + chr6_1:18359687-18359706 Msa0878010:CDS 30.0%
TATCAGATTCACTCAATTGA+CGG - chr6_1:18359853-18359872 None:intergenic 30.0%
! TGTTAGAACCTGTCATATTT+TGG + chr6_1:18359904-18359923 Msa0878010:CDS 30.0%
! GTTAGAACCTGTCATATTTT+GGG + chr6_1:18359905-18359924 Msa0878010:CDS 30.0%
CATAAAACCCAAAATATGAC+AGG - chr6_1:18359915-18359934 None:intergenic 30.0%
CTACTTATACAATGAAGGAA+AGG + chr6_1:18359991-18360010 Msa0878010:CDS 30.0%
ATTTATGTCTCCATCGTTTG+CGG - chr6_1:18359405-18359424 None:intergenic 35.0%
TGAAGAAGGAAAAGAGGATA+TGG + chr6_1:18359460-18359479 Msa0878010:CDS 35.0%
CAAGAAGATTAGGGAATTGA+CGG + chr6_1:18359490-18359509 Msa0878010:CDS 35.0%
! TTGACGGATGATGATATAAG+AGG + chr6_1:18359506-18359525 Msa0878010:CDS 35.0%
GGATGATGATATAAGAGGAT+TGG + chr6_1:18359511-18359530 Msa0878010:CDS 35.0%
GAAATCTATGCAGATTGTCA+TGG + chr6_1:18359569-18359588 Msa0878010:CDS 35.0%
ACTAATAAGTGGAGAGTTTC+TGG + chr6_1:18359764-18359783 Msa0878010:CDS 35.0%
TAGGAACCAAATGAGCATAA+CGG - chr6_1:18359826-18359845 None:intergenic 35.0%
GAAGGAAAGGTAAGAATAGA+AGG + chr6_1:18360004-18360023 Msa0878010:CDS 35.0%
GCAAACGATGGAGACATAAA+TGG + chr6_1:18359404-18359423 Msa0878010:CDS 40.0%
AATGGTGAAGATTTAGCCAG+CGG + chr6_1:18359422-18359441 Msa0878010:CDS 40.0%
ATTAAACACACCATTACCGC+TGG - chr6_1:18359441-18359460 None:intergenic 40.0%
TGCAGAACACTTAGTTCGAA+TGG - chr6_1:18359717-18359736 None:intergenic 40.0%
TTCGAACTAAGTGTTCTGCA+AGG + chr6_1:18359717-18359736 Msa0878010:CDS 40.0%
GTTAACTCATGGTTGTGTGA+GGG - chr6_1:18359797-18359816 None:intergenic 40.0%
AGTTAACTCATGGTTGTGTG+AGG - chr6_1:18359798-18359817 None:intergenic 40.0%
AGGAACCAAATGAGCATAAC+GGG - chr6_1:18359825-18359844 None:intergenic 40.0%
TCACTCAATTGACGGTTCTT+AGG - chr6_1:18359845-18359864 None:intergenic 40.0%
TCTGATAAAGCCCTTGTTGA+TGG + chr6_1:18359866-18359885 Msa0878010:CDS 40.0%
TGCATGAAGACCATCAACAA+GGG - chr6_1:18359879-18359898 None:intergenic 40.0%
!! GGTTTTATGATGGCTCAGAA+AGG + chr6_1:18359926-18359945 Msa0878010:CDS 40.0%
TTTATGATGGCTCAGAAAGG+AGG + chr6_1:18359929-18359948 Msa0878010:CDS 40.0%
GGAAAGGTAAGAATAGAAGG+TGG + chr6_1:18360007-18360026 Msa0878010:CDS 40.0%
GAAGATTTAGCCAGCGGTAA+TGG + chr6_1:18359428-18359447 Msa0878010:CDS 45.0%
TGCAGATTGTCATGGGTTTG+TGG + chr6_1:18359577-18359596 Msa0878010:CDS 45.0%
!! AACGGGTTGGAGTTAACTCA+TGG - chr6_1:18359808-18359827 None:intergenic 45.0%
TCCAACCCGTTATGCTCATT+TGG + chr6_1:18359817-18359836 Msa0878010:CDS 45.0%
!! ACCAAATGAGCATAACGGGT+TGG - chr6_1:18359821-18359840 None:intergenic 45.0%
GTGCATGAAGACCATCAACA+AGG - chr6_1:18359880-18359899 None:intergenic 45.0%
!! GTTGATGGTCTTCATGCACA+CGG + chr6_1:18359881-18359900 Msa0878010:CDS 45.0%
AAAGGAGGTCATGAGAGTCT+GGG + chr6_1:18359944-18359963 Msa0878010:CDS 45.0%
!! ATGAGAGTCTGGGATTTTGC+AGG + chr6_1:18359954-18359973 Msa0878010:CDS 45.0%
GAAAGGAGGTCATGAGAGTC+TGG + chr6_1:18359943-18359962 Msa0878010:CDS 50.0%
!! GAGTCTGGGATTTTGCAGGA+AGG + chr6_1:18359958-18359977 Msa0878010:CDS 50.0%
Chromosome Type Strat End Strand Name
chr6_1 gene 18359398 18360060 18359398 ID=Msa0878010;Name=Msa0878010
chr6_1 mRNA 18359398 18360060 18359398 ID=Msa0878010-mRNA-1;Parent=Msa0878010;Name=Msa0878010-mRNA-1;_AED=0.40;_eAED=0.42;_QI=0|-1|0|1|-1|1|1|0|220
chr6_1 exon 18359398 18360060 18359398 ID=Msa0878010-mRNA-1:exon:4995;Parent=Msa0878010-mRNA-1
chr6_1 CDS 18359398 18360060 18359398 ID=Msa0878010-mRNA-1:cds;Parent=Msa0878010-mRNA-1
Gene Sequence

>Msa0878010

ATGGCCGCAAACGATGGAGACATAAATGGTGAAGATTTAGCCAGCGGTAATGGTGTGTTTAATGAAGAAGGAAAAGAGGATATGGATACTTACAAGAAGATTAGGGAATTGACGGATGATGATATAAGAGGATTGGAATTTGATTCAGAGCAAAAAGCGACACAATTTTATGAAATCTATGCAGATTGTCATGGGTTTGTGGTAAGAAAAGATGATGTAAACAAAGATGATGATGGGAATATAATTGCACGTCGATTAGTATGTAATAGAGAGGGTGAGAATAAAAATAAGAAACAAAGTACATATTCGAGGCAGACCATTCGAACTAAGTGTTCTGCAAGGCTTCGAGTAGTTTTAAATGTTGATACTAATAAGTGGAGAGTTTCTGGATTCGAGCCCTCACACAACCATGAGTTAACTCCAACCCGTTATGCTCATTTGGTTCCTAAGAACCGTCAATTGAGTGAATCTGATAAAGCCCTTGTTGATGGTCTTCATGCACACGGTGTTAGAACCTGTCATATTTTGGGTTTTATGATGGCTCAGAAAGGAGGTCATGAGAGTCTGGGATTTTGCAGGAAGGACTTATATAACTACTTATACAATGAAGGAAAGGTAAGAATAGAAGGTGGAGATTCTTTTGCTGCGTTGAGTTATTTGTAG
Protein sequence

>Msa0878010

MAANDGDINGEDLASGNGVFNEEGKEDMDTYKKIRELTDDDIRGLEFDSEQKATQFYEIYADCHGFVVRKDDVNKDDDGNIIARRLVCNREGENKNKKQSTYSRQTIRTKCSARLRVVLNVDTNKWRVSGFEPSHNHELTPTRYAHLVPKNRQLSESDKALVDGLHAHGVRTCHILGFMMAQKGGHESLGFCRKDLYNYLYNEGKVRIEGGDSFAALSYL*