AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1459970

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1459970 MtrunA17_Chr4g0007031 98.450 129 2 0 1 129 93 221 1.98e-90 261
Msa1459970 MtrunA17_Chr4g0007051 98.450 129 2 0 1 129 93 221 1.98e-90 261
Msa1459970 MtrunA17_Chr5g0419971 98.450 129 2 0 1 129 93 221 1.98e-90 261
Msa1459970 MtrunA17_Chr5g0419981 98.450 129 2 0 1 129 93 221 1.98e-90 261
Msa1459970 MtrunA17_Chr2g0285871 98.450 129 2 0 1 129 93 221 4.41e-90 260
Msa1459970 MtrunA17_Chr4g0007041 97.674 129 3 0 1 129 93 221 8.88e-90 259
Msa1459970 MtrunA17_Chr1g0189841 86.047 129 18 0 1 129 94 222 5.14e-79 232
Msa1459970 MtrunA17_Chr6g0449771 83.721 129 20 1 1 129 93 220 8.54e-73 216
Msa1459970 MtrunA17_Chr6g0449751 83.721 129 20 1 1 129 93 220 8.92e-73 216
Msa1459970 MtrunA17_Chr6g0449731 83.594 128 20 1 1 128 93 219 5.73e-72 214
Msa1459970 MtrunA17_Chr6g0449761 84.000 125 19 1 1 125 93 216 3.32e-70 211
Msa1459970 MtrunA17_Chr6g0449781 71.318 129 35 2 1 129 93 219 4.91e-57 176
Msa1459970 MtrunA17_Chr1g0156131 65.854 123 41 1 1 123 87 208 1.24e-53 167
Msa1459970 MtrunA17_Chr2g0292831 64.228 123 43 1 1 123 90 211 1.28e-53 167
Msa1459970 MtrunA17_Chr2g0292901 65.041 123 42 1 1 123 91 212 9.26e-53 165
Msa1459970 MtrunA17_Chr2g0292861 63.710 124 43 2 1 123 55 177 1.18e-51 161
Msa1459970 MtrunA17_Chr2g0292841 63.710 124 43 2 1 123 55 177 1.73e-50 158
Msa1459970 MtrunA17_Chr6g0449791 66.379 116 39 0 1 116 93 208 7.62e-50 157
Msa1459970 MtrunA17_Chr1g0193671 47.967 123 61 1 1 123 94 213 2.99e-39 131
Msa1459970 MtrunA17_Chr1g0193421 46.341 123 63 1 1 123 95 214 1.10e-34 119
Msa1459970 MtrunA17_Chr7g0271211 48.780 123 60 1 1 123 91 210 2.48e-34 118
Msa1459970 MtrunA17_Chr1g0210761 47.154 123 60 2 1 123 89 206 1.41e-32 114
Msa1459970 MtrunA17_Chr5g0414971 45.968 124 63 2 1 123 98 218 9.69e-31 109
Msa1459970 MtrunA17_Chr2g0292911 67.606 71 22 1 1 71 55 124 3.16e-28 100
Msa1459970 MtrunA17_Chr1g0178711 41.463 123 67 2 1 123 103 220 5.44e-28 102
Msa1459970 MtrunA17_Chr2g0321581 43.443 122 63 3 2 122 86 202 1.40e-27 100
Msa1459970 MtrunA17_Chr2g0300561 43.802 121 63 2 1 121 88 203 1.64e-27 100
Msa1459970 MtrunA17_Chr2g0321601 43.443 122 63 3 2 122 85 201 2.30e-27 100
Msa1459970 MtrunA17_Chr2g0321591 42.623 122 64 3 2 122 86 202 4.43e-27 99.8
Msa1459970 MtrunA17_Chr4g0026201 43.443 122 63 3 2 122 87 203 3.54e-26 97.4
Msa1459970 MtrunA17_Chr4g0026191 43.443 122 63 3 2 122 87 203 5.61e-26 97.1
Msa1459970 MtrunA17_Chr8g0344021 51.064 94 42 1 2 95 92 181 9.98e-25 93.6
Msa1459970 MtrunA17_Chr2g0300581 39.344 122 69 2 1 122 88 204 7.00e-24 91.7
Msa1459970 MtrunA17_Chr2g0300591 39.669 121 68 2 1 121 88 203 7.87e-24 91.3
Msa1459970 MtrunA17_Chr8g0343911 40.496 121 67 2 2 122 87 202 2.54e-22 87.4
Msa1459970 MtrunA17_Chr2g0292881 67.241 58 18 1 1 58 1 57 1.48e-20 79.0
Msa1459970 MtrunA17_Chr2g0297231 41.525 118 58 3 2 114 89 200 1.06e-19 80.5
Msa1459970 MtrunA17_Chr2g0297241 46.988 83 40 1 3 85 90 168 1.10e-19 80.5
Msa1459970 MtrunA17_Chr3g0084531 41.748 103 55 2 3 105 90 187 1.91e-19 80.1
Msa1459970 MtrunA17_Chr3g0084511 41.748 103 55 2 3 105 89 186 2.12e-19 79.7
Msa1459970 MtrunA17_Chr2g0313961 46.988 83 40 1 3 85 90 168 2.65e-19 79.7
Msa1459970 MtrunA17_Chr3g0084521 41.748 103 55 2 3 105 89 186 2.65e-19 79.7
Msa1459970 MtrunA17_Chr8g0343954 34.426 122 74 2 2 123 89 204 5.16e-19 79.0
Msa1459970 MtrunA17_Chr8g0343934 43.023 86 45 1 2 87 89 170 7.48e-19 78.6
Msa1459970 MtrunA17_Chr8g0344041 38.793 116 64 2 2 114 93 204 9.05e-19 78.2
Msa1459970 MtrunA17_Chr8g0343961 43.023 86 45 1 2 87 89 170 2.37e-18 77.0
Msa1459970 MtrunA17_Chr2g0302171 43.529 85 44 1 1 85 88 168 2.87e-18 77.0
Msa1459970 MtrunA17_Chr8g0335851 37.398 123 67 2 1 123 98 210 4.54e-18 76.6
Msa1459970 MtrunA17_Chr8g0344051 47.619 84 40 1 1 84 91 170 6.15e-18 76.3
Msa1459970 MtrunA17_Chr2g0301611 44.578 83 42 1 3 85 90 168 6.28e-18 75.9
Msa1459970 MtrunA17_Chr4g0003361 37.705 122 69 3 2 123 86 200 1.99e-17 74.7
Msa1459970 MtrunA17_Chr8g0343921 35.833 120 72 2 2 121 86 200 3.81e-17 73.9
Msa1459970 MtrunA17_Chr2g0302541 43.529 85 44 1 3 87 90 170 1.43e-16 72.4
Msa1459970 MtrunA17_Chr2g0286171 34.426 122 74 2 2 123 92 207 1.63e-16 72.4
Msa1459970 MtrunA17_Chr8g0344031 37.705 122 70 2 2 123 91 206 7.59e-16 70.5
Msa1459970 MtrunA17_Chr4g0012651 37.391 115 65 2 3 114 90 200 7.83e-16 70.5
Msa1459970 MtrunA17_Chr7g0217811 37.391 115 65 2 3 114 90 200 1.30e-15 70.1
Msa1459970 MtrunA17_Chr5g0411961 40.000 85 47 1 3 87 90 170 2.14e-15 69.3
Msa1459970 MtrunA17_Chr3g0130241 42.529 87 47 1 1 87 161 244 4.07e-15 69.7
Msa1459970 MtrunA17_Chr3g0115141 35.345 116 68 2 2 114 90 201 4.49e-15 68.6
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1459970 AT3G05950.1 67.176 131 41 1 1 129 98 228 2.59e-58 180
Msa1459970 AT5G39160.2 67.480 123 40 0 1 123 74 196 9.29e-57 175
Msa1459970 AT5G39190.2 67.480 123 40 0 1 123 74 196 1.09e-56 175
Msa1459970 AT5G39160.3 67.480 123 40 0 1 123 92 214 2.36e-56 175
Msa1459970 AT5G39160.1 67.480 123 40 0 1 123 96 218 3.17e-56 174
Msa1459970 AT5G39190.1 67.480 123 40 0 1 123 96 218 3.38e-56 174
Msa1459970 AT5G39130.1 65.854 123 42 0 1 123 96 218 1.27e-55 173
Msa1459970 AT5G39150.1 64.228 123 44 0 1 123 96 218 3.24e-54 169
Msa1459970 AT5G39110.1 64.228 123 44 0 1 123 97 219 4.52e-54 169
Msa1459970 AT5G39120.1 64.228 123 44 0 1 123 96 218 5.11e-54 169
Msa1459970 AT5G39180.1 64.228 123 44 0 1 123 96 218 6.50e-54 169
Msa1459970 AT3G04200.1 65.289 121 42 0 1 121 99 219 2.77e-52 165
Msa1459970 AT4G14630.1 62.602 123 46 0 1 123 99 221 1.27e-49 158
Msa1459970 AT5G38940.1 62.602 123 45 1 1 123 99 220 7.29e-49 156
Msa1459970 AT5G38940.2 62.602 123 45 1 1 123 123 244 1.42e-48 156
Msa1459970 AT5G38930.1 64.228 123 43 1 1 123 99 220 1.67e-48 155
Msa1459970 AT5G38960.1 63.415 123 44 1 1 123 100 221 2.68e-46 149
Msa1459970 AT3G04190.1 59.504 121 49 0 1 121 98 218 1.26e-45 147
Msa1459970 AT5G38910.1 61.789 123 46 1 1 123 97 218 1.01e-44 145
Msa1459970 AT3G04180.1 57.025 121 52 0 1 121 98 218 2.80e-44 144
Msa1459970 AT3G04170.1 56.557 122 53 0 1 122 95 216 1.26e-43 142
Msa1459970 AT3G04150.1 52.459 122 58 0 1 122 98 219 1.63e-40 135
Msa1459970 AT3G04150.2 52.459 122 58 0 1 122 111 232 1.84e-40 135
Msa1459970 AT1G02335.1 50.407 123 58 1 1 123 95 214 5.03e-40 133
Msa1459970 AT1G09560.1 47.967 123 61 1 1 123 95 214 1.84e-35 122
Msa1459970 AT3G62020.2 49.194 124 59 2 1 123 65 185 2.24e-35 120
Msa1459970 AT3G62020.1 49.194 124 59 2 1 123 94 214 5.17e-35 120
Msa1459970 AT1G18970.1 45.833 120 62 1 4 123 101 217 2.09e-34 119
Msa1459970 AT5G26700.1 51.786 112 48 2 1 112 92 197 3.30e-34 118
Msa1459970 AT1G18980.1 47.500 120 60 1 4 123 101 217 4.80e-34 118
Msa1459970 AT3G05930.1 50.909 110 51 1 1 110 95 201 9.73e-33 114
Msa1459970 AT3G10080.1 42.276 123 66 2 1 123 101 218 2.34e-29 106
Msa1459970 AT3G10080.2 42.276 123 66 2 1 123 172 289 1.06e-28 106
Msa1459970 AT1G10460.1 42.742 124 67 2 1 123 94 214 6.66e-28 102
Msa1459970 AT5G20630.1 42.241 116 63 2 1 116 89 200 2.85e-24 92.8
Msa1459970 AT5G61750.1 44.681 94 49 1 1 94 92 182 1.03e-21 86.3
Msa1459970 AT1G74820.1 36.585 123 75 1 1 123 105 224 1.25e-21 86.3
Msa1459970 AT1G72610.1 39.167 120 68 3 2 121 87 201 3.12e-21 85.1
Msa1459970 AT5G38910.2 41.463 123 34 1 1 123 97 181 8.23e-21 83.2
Msa1459970 AT5G38950.1 54.167 72 33 0 53 124 2 73 1.17e-19 78.2

Find 30 sgRNAs with CRISPR-Local

Find 35 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTTCAATTGAATGTGGGATA+TGG 0.265965 tig0040567:-17795 Msa1459970:CDS
CTTATCCACTTGAAAAGCTT+TGG 0.335788 tig0040567:+17668 None:intergenic
GAGACGATTGTTGTCTTGAT+TGG 0.345597 tig0040567:+17875 None:intergenic
TGAAAATGAATAAGACCAAT+TGG 0.350439 tig0040567:+17813 None:intergenic
GAGTGCCTTCGAGTACTATA+AGG 0.397511 tig0040567:+17919 None:intergenic
GGCAACGCTGTTGCTATTGC+TGG 0.409649 tig0040567:-17774 Msa1459970:CDS
GATGTGTTTGTGTTCCCAAT+TGG 0.424230 tig0040567:-17828 Msa1459970:CDS
ATTATCTTCAAAAGCAGTCT+TGG 0.442184 tig0040567:-17635 Msa1459970:CDS
CTCGAAGGCACTCTTTATGT+TGG 0.443268 tig0040567:-17909 Msa1459970:CDS
ATCACCCTTGTTTAGCACTT+TGG 0.448300 tig0040567:+17848 None:intergenic
CCCTAGGGTGAATGTGAGGT+GGG 0.472883 tig0040567:+17952 None:intergenic
TTTGCAACAGTGATAACTCC+TGG 0.481242 tig0040567:+17735 None:intergenic
GAAAATGAATAAGACCAATT+GGG 0.506436 tig0040567:+17814 None:intergenic
ATAAGGATCTCTGTTCCCCT+AGG 0.521648 tig0040567:+17936 None:intergenic
TGAGGTGGGTTTAAACCCTT+AGG 0.548128 tig0040567:+17966 None:intergenic
CCCACCTCACATTCACCCTA+GGG 0.554780 tig0040567:-17952 Msa1459970:CDS
CCCCTAGGGTGAATGTGAGG+TGG 0.562730 tig0040567:+17951 None:intergenic
TTGCAACAGTGATAACTCCT+GGG 0.567087 tig0040567:+17736 None:intergenic
GAACCTCGTCGGAAATAAGC+GGG 0.573571 tig0040567:+17694 None:intergenic
CTTCACCAAAGTGCTAAACA+AGG 0.580133 tig0040567:-17853 Msa1459970:CDS
AGAACCTCGTCGGAAATAAG+CGG 0.593140 tig0040567:+17693 None:intergenic
ACCCACCTCACATTCACCCT+AGG 0.594952 tig0040567:-17953 Msa1459970:CDS
AGCTTTGGTAAGAACCTCGT+CGG 0.612864 tig0040567:+17683 None:intergenic
TAAGGATCTCTGTTCCCCTA+GGG 0.621607 tig0040567:+17937 None:intergenic
GTTCCCCTAGGGTGAATGTG+AGG 0.650118 tig0040567:+17948 None:intergenic
GAGATCCTTATAGTACTCGA+AGG 0.666965 tig0040567:-17924 Msa1459970:CDS
TTCACCAAAGTGCTAAACAA+GGG 0.675942 tig0040567:-17852 Msa1459970:CDS
GGACTTAGCAGTCAAAACCC+AGG 0.692136 tig0040567:-17753 Msa1459970:CDS
TGACCCGCTTATTTCCGACG+AGG 0.709948 tig0040567:-17697 Msa1459970:CDS
CCACCTCACATTCACCCTAG+GGG 0.723455 tig0040567:-17951 Msa1459970:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TATTCATTTTCAATTGAATG+TGG - tig0040567:17805-17824 Msa1459970:CDS 20.0%
!!! ATTCATTTTCAATTGAATGT+GGG - tig0040567:17806-17825 Msa1459970:CDS 20.0%
! GAAAATGAATAAGACCAATT+GGG + tig0040567:17796-17815 None:intergenic 25.0%
! TGAAAATGAATAAGACCAAT+TGG + tig0040567:17797-17816 None:intergenic 25.0%
TTTCAATTGAATGTGGGATA+TGG - tig0040567:17812-17831 Msa1459970:CDS 30.0%
ATTATCTTCAAAAGCAGTCT+TGG - tig0040567:17972-17991 Msa1459970:CDS 30.0%
! TTCACCAAAGTGCTAAACAA+GGG - tig0040567:17755-17774 Msa1459970:CDS 35.0%
!! TCTTACCAAAGCTTTTCAAG+TGG - tig0040567:17934-17953 Msa1459970:CDS 35.0%
CTTATCCACTTGAAAAGCTT+TGG + tig0040567:17942-17961 None:intergenic 35.0%
!!! TCGCATTGATTTTGTGCCTA+AGG - tig0040567:17625-17644 Msa1459970:CDS 40.0%
!!! CGCATTGATTTTGTGCCTAA+GGG - tig0040567:17626-17645 Msa1459970:CDS 40.0%
GAGATCCTTATAGTACTCGA+AGG - tig0040567:17683-17702 Msa1459970:CDS 40.0%
GAGACGATTGTTGTCTTGAT+TGG + tig0040567:17735-17754 None:intergenic 40.0%
! CTTCACCAAAGTGCTAAACA+AGG - tig0040567:17754-17773 Msa1459970:CDS 40.0%
! ATCACCCTTGTTTAGCACTT+TGG + tig0040567:17762-17781 None:intergenic 40.0%
GATGTGTTTGTGTTCCCAAT+TGG - tig0040567:17779-17798 Msa1459970:CDS 40.0%
TTGCAACAGTGATAACTCCT+GGG + tig0040567:17874-17893 None:intergenic 40.0%
TTTGCAACAGTGATAACTCC+TGG + tig0040567:17875-17894 None:intergenic 40.0%
! TGAGGTGGGTTTAAACCCTT+AGG + tig0040567:17644-17663 None:intergenic 45.0%
TAAGGATCTCTGTTCCCCTA+GGG + tig0040567:17673-17692 None:intergenic 45.0%
ATAAGGATCTCTGTTCCCCT+AGG + tig0040567:17674-17693 None:intergenic 45.0%
GAGTGCCTTCGAGTACTATA+AGG + tig0040567:17691-17710 None:intergenic 45.0%
!! CTCGAAGGCACTCTTTATGT+TGG - tig0040567:17698-17717 Msa1459970:CDS 45.0%
AGAACCTCGTCGGAAATAAG+CGG + tig0040567:17917-17936 None:intergenic 45.0%
! AGCTTTGGTAAGAACCTCGT+CGG + tig0040567:17927-17946 None:intergenic 45.0%
GGACTTAGCAGTCAAAACCC+AGG - tig0040567:17854-17873 Msa1459970:CDS 50.0%
GAACCTCGTCGGAAATAAGC+GGG + tig0040567:17916-17935 None:intergenic 50.0%
ACCCACCTCACATTCACCCT+AGG - tig0040567:17654-17673 Msa1459970:CDS 55.0%
CCCTAGGGTGAATGTGAGGT+GGG + tig0040567:17658-17677 None:intergenic 55.0%
CCCACCTCACATTCACCCTA+GGG - tig0040567:17655-17674 Msa1459970:CDS 55.0%
CCACCTCACATTCACCCTAG+GGG - tig0040567:17656-17675 Msa1459970:CDS 55.0%
GTTCCCCTAGGGTGAATGTG+AGG + tig0040567:17662-17681 None:intergenic 55.0%
! GGCAACGCTGTTGCTATTGC+TGG - tig0040567:17833-17852 Msa1459970:CDS 55.0%
TGACCCGCTTATTTCCGACG+AGG - tig0040567:17910-17929 Msa1459970:CDS 55.0%
CCCCTAGGGTGAATGTGAGG+TGG + tig0040567:17659-17678 None:intergenic 60.0%
Chromosome Type Strat End Strand Name
tig0040567 gene 17620 18009 17620 ID=Msa1459970;Name=Msa1459970
tig0040567 mRNA 17620 18009 17620 ID=Msa1459970-mRNA-1;Parent=Msa1459970;Name=Msa1459970-mRNA-1;_AED=0.04;_eAED=0.04;_QI=0|-1|0|1|-1|1|1|0|129
tig0040567 exon 17620 18009 17620 ID=Msa1459970-mRNA-1:exon:22497;Parent=Msa1459970-mRNA-1
tig0040567 CDS 17620 18009 17620 ID=Msa1459970-mRNA-1:cds;Parent=Msa1459970-mRNA-1
Gene Sequence

>Msa1459970

TTGGCTCGCATTGATTTTGTGCCTAAGGGTTTAAACCCACCTCACATTCACCCTAGGGGAACAGAGATCCTTATAGTACTCGAAGGCACTCTTTATGTTGGATTTGTCACGTCCAATCAAGACAACAATCGTCTCTTCACCAAAGTGCTAAACAAGGGTGATGTGTTTGTGTTCCCAATTGGTCTTATTCATTTTCAATTGAATGTGGGATATGGCAACGCTGTTGCTATTGCTGGACTTAGCAGTCAAAACCCAGGAGTTATCACTGTTGCAAATGCTTTGTTTAAATCTGACCCGCTTATTTCCGACGAGGTTCTTACCAAAGCTTTTCAAGTGGATAAGAGCATAATTGATTATCTTCAAAAGCAGTCTTGGTATGACAACAACTAG
Protein sequence

>Msa1459970

LARIDFVPKGLNPPHIHPRGTEILIVLEGTLYVGFVTSNQDNNRLFTKVLNKGDVFVFPIGLIHFQLNVGYGNAVAIAGLSSQNPGVITVANALFKSDPLISDEVLTKAFQVDKSIIDYLQKQSWYDNN*