AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0097340

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0097340 MtrunA17_Chr1g0152661 94.538 238 6 3 1 237 1 232 7.85e-167 459
Msa0097340 MtrunA17_Chr3g0134711 57.028 249 78 9 1 235 1 234 3.37e-82 245
Msa0097340 MtrunA17_Chr1g0207451 43.071 267 84 13 1 226 3 242 5.07e-47 156
Msa0097340 MtrunA17_Chr1g0180311 37.113 194 88 9 43 205 81 271 2.75e-21 90.1
Msa0097340 MtrunA17_Chr4g0012691 48.837 86 42 1 80 165 220 303 9.77e-18 81.3
Msa0097340 MtrunA17_Chr7g0263121 36.667 120 56 2 43 162 15 114 2.58e-17 76.6
Msa0097340 MtrunA17_Chr7g0231181 38.298 141 60 6 71 211 231 344 3.10e-17 79.7
Msa0097340 MtrunA17_Chr1g0197281 28.829 222 112 7 21 198 81 300 2.90e-16 76.6
Msa0097340 MtrunA17_Chr7g0263131 36.364 121 66 2 80 200 34 143 5.23e-16 73.2
Msa0097340 MtrunA17_Chr2g0320311 30.952 210 98 6 39 201 71 280 8.13e-16 75.1
Msa0097340 MtrunA17_Chr5g0425411 47.253 91 43 2 79 164 118 208 1.39e-15 73.6
Msa0097340 MtrunA17_Chr7g0222831 34.058 138 67 4 32 169 2 115 3.16e-15 71.2
Msa0097340 MtrunA17_Chr1g0182161 29.070 172 89 4 32 196 3 148 6.82e-15 70.1
Msa0097340 MtrunA17_Chr1g0212561 43.373 83 38 2 80 162 45 118 1.72e-14 69.7
Msa0097340 MtrunA17_Chr5g0448611 41.441 111 38 3 80 166 130 237 2.52e-14 70.5
Msa0097340 MtrunA17_Chr1g0182181 32.609 138 64 3 38 173 6 116 1.54e-13 66.2
Msa0097340 MtrunA17_Chr4g0027991 29.878 164 70 4 44 162 67 230 5.50e-13 67.0
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0097340 AT1G27730.1 50.000 248 88 11 1 233 1 227 3.41e-60 189
Msa0097340 AT5G04340.1 51.304 230 96 8 1 217 1 227 1.25e-51 168
Msa0097340 AT3G19580.1 41.176 255 102 7 1 214 1 248 2.09e-46 155
Msa0097340 AT3G19580.2 41.176 255 102 7 1 214 1 248 2.09e-46 155
Msa0097340 AT5G43170.1 45.148 237 73 11 1 225 1 192 5.28e-42 142
Msa0097340 AT5G67450.1 39.834 241 98 7 1 198 1 237 1.78e-36 129
Msa0097340 AT3G49930.1 43.069 202 69 8 25 211 36 206 8.74e-36 126
Msa0097340 AT2G28200.1 37.113 194 92 7 37 201 70 262 1.40e-24 99.0
Msa0097340 AT3G60580.1 37.500 184 83 5 38 211 122 283 2.57e-23 95.9
Msa0097340 AT2G45120.1 39.286 168 82 5 38 198 146 300 3.40e-22 93.2
Msa0097340 AT1G49900.1 51.111 90 36 2 80 169 193 274 3.87e-20 89.4
Msa0097340 AT1G49900.1 46.667 105 41 3 79 181 749 840 9.83e-20 88.2
Msa0097340 AT5G03510.1 31.250 192 102 4 39 201 69 259 1.35e-18 83.2
Msa0097340 AT5G56200.1 46.237 93 37 2 82 163 344 434 4.12e-17 80.1
Msa0097340 AT5G04390.1 28.879 232 113 8 39 233 96 312 4.14e-17 79.7
Msa0097340 AT1G02040.1 32.105 190 96 7 5 163 61 248 5.45e-17 79.0
Msa0097340 AT4G35280.1 39.231 130 54 5 39 164 138 246 2.21e-16 76.6
Msa0097340 AT2G37430.1 37.037 135 61 4 32 162 2 116 1.54e-15 72.4
Msa0097340 AT3G53600.1 31.579 171 89 7 32 196 2 150 1.90e-14 69.3
Msa0097340 AT3G46090.1 34.091 132 60 3 38 169 11 115 1.91e-14 69.3
Msa0097340 AT1G02030.1 43.373 83 36 2 80 162 160 231 1.94e-14 71.2
Msa0097340 AT2G28710.1 35.833 120 44 3 43 162 14 100 2.60e-14 68.6
Msa0097340 AT2G17180.1 30.909 165 76 5 39 198 121 252 4.22e-14 70.1
Msa0097340 AT3G46080.1 43.023 86 37 1 77 162 34 107 1.68e-12 63.9
Msa0097340 AT5G61470.1 40.000 85 35 2 80 163 228 297 1.68e-12 66.2
Msa0097340 AT3G10470.1 30.556 180 69 4 39 162 104 283 1.77e-12 66.6
Msa0097340 AT5G59820.1 34.328 134 54 6 46 176 18 120 5.09e-12 62.8
Msa0097340 AT3G46070.1 36.957 92 48 2 71 162 27 108 4.30e-11 60.1

Find 61 sgRNAs with CRISPR-Local

Find 67 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GGTTCATCGAAGGTGAATTT+AGG 0.179252 1_3:-3146600 None:intergenic
CGTTTAGTCCATGGAAGATT+AGG 0.289571 1_3:-3146621 None:intergenic
AAAATTCGGAATTTCAATCT+TGG 0.317164 1_3:-3147246 None:intergenic
AGAACATTTGTAACTGAGTT+TGG 0.333314 1_3:-3146787 None:intergenic
CCGGAGTTTGCTAATAAGAT+TGG 0.334097 1_3:+3147158 Msa0097340:CDS
ATTATTCATCACTGAAAATT+CGG 0.339013 1_3:-3147260 None:intergenic
GTTCATCGAAGGTGAATTTA+GGG 0.339272 1_3:-3146599 None:intergenic
TTGTCAATGGTTGTTGGTGG+TGG 0.368111 1_3:-3146753 None:intergenic
TTTCCGACAGGACAAGCTTT+GGG 0.386450 1_3:+3147005 Msa0097340:CDS
AAATTCGGAATTTCAATCTT+GGG 0.411878 1_3:-3147245 None:intergenic
TCTGAATATCCCGGCTTATC+CGG 0.414206 1_3:+3147139 Msa0097340:CDS
AACTCCGTCGGTGGCGGTGT+TGG 0.416768 1_3:+3146873 Msa0097340:CDS
GTTTCCGACAGGACAAGCTT+TGG 0.428305 1_3:+3147004 Msa0097340:CDS
GATTCAAAGGCTTGAAATCA+TGG 0.448405 1_3:-3146731 None:intergenic
TTCTTCATCATCACAGGATG+AGG 0.458403 1_3:-3147200 None:intergenic
TTGTTGTTGTCAATGGTTGT+TGG 0.473433 1_3:-3146759 None:intergenic
GCTTTCTTCTTCATCATCAC+AGG 0.490449 1_3:-3147206 None:intergenic
TTAGCAAACTCCGGATAAGC+CGG 0.495798 1_3:-3147149 None:intergenic
ATGAGTGTTCGATTTGTCAT+AGG 0.501927 1_3:+3146979 Msa0097340:CDS
ACTTGCTTTGTGTCCACCGA+GGG 0.502207 1_3:-3146841 None:intergenic
GTCGGTGGCGGTGTTGGTGT+TGG 0.503000 1_3:+3146879 Msa0097340:CDS
TGTCATAGGTCGTTTCCGAC+AGG 0.511441 1_3:+3146993 Msa0097340:CDS
TTGTTGTCAATGGTTGTTGG+TGG 0.511574 1_3:-3146756 None:intergenic
GAATTTAGGGGTAGTAGAAG+TGG 0.512596 1_3:-3146586 None:intergenic
GAACGTTTACGTTTAGTCCA+TGG 0.526324 1_3:-3146630 None:intergenic
GTGGCAGCTGAGGAAGTTGG+TGG 0.531004 1_3:-3146915 None:intergenic
GGTGGCGGTGTTGGTGTTGG+TGG 0.533807 1_3:+3146882 Msa0097340:CDS
GTTGTTGGTGGTGGATTCAA+AGG 0.535966 1_3:-3146744 None:intergenic
TGTCACTACGAAGGTGTTGT+TGG 0.546239 1_3:+3147041 Msa0097340:CDS
AATTTAGGGGTAGTAGAAGT+GGG 0.550780 1_3:-3146585 None:intergenic
CCAATCTTATTAGCAAACTC+CGG 0.554584 1_3:-3147158 None:intergenic
CCACCCAAAGCTTGTCCTGT+CGG 0.557784 1_3:-3147008 None:intergenic
CACTACGAAGGTGTTGTTGG+TGG 0.560111 1_3:+3147044 Msa0097340:CDS
TACGAAGGTGTTGTTGGTGG+TGG 0.560220 1_3:+3147047 Msa0097340:CDS
AACACCGCCACCGTTTGTGT+TGG 0.560436 1_3:-3146949 None:intergenic
ACTAGCTCAGCCAACACAAA+CGG 0.565002 1_3:+3146939 Msa0097340:CDS
TCGATGAACCTAATCTTCCA+TGG 0.566526 1_3:+3146613 Msa0097340:CDS
TGAGCTAGTGGTGGCAGCTG+AGG 0.573892 1_3:-3146925 None:intergenic
TGATTTCGATCTGAATATCC+CGG 0.576158 1_3:+3147130 Msa0097340:CDS
GTGGTGGCAGCTGAGGAAGT+TGG 0.576892 1_3:-3146918 None:intergenic
CCGACAGGACAAGCTTTGGG+TGG 0.581171 1_3:+3147008 Msa0097340:CDS
TGAAATCATGGCGGTTGGTG+TGG 0.583151 1_3:-3146719 None:intergenic
AGGCTTGAAATCATGGCGGT+TGG 0.583949 1_3:-3146724 None:intergenic
TAGCAAACTCCGGATAAGCC+GGG 0.583949 1_3:-3147148 None:intergenic
TCTGCTATAACTGTCTCTGA+AGG 0.590024 1_3:+3147080 Msa0097340:CDS
TGTCTCATCATGCTCGCTCG+TGG 0.591916 1_3:+3146696 Msa0097340:CDS
TATAACTGTCTCTGAAGGTG+TGG 0.592472 1_3:+3147085 Msa0097340:CDS
TGGCAGCTGAGGAAGTTGGT+GGG 0.594864 1_3:-3146914 None:intergenic
AACACCAACACCGCCACCGA+CGG 0.603987 1_3:-3146877 None:intergenic
ATAACTGTCTCTGAAGGTGT+GGG 0.609017 1_3:+3147086 Msa0097340:CDS
TCAGCCAACACAAACGGTGG+CGG 0.610808 1_3:+3146945 Msa0097340:CDS
GACTTGCTTTGTGTCCACCG+AGG 0.621099 1_3:-3146842 None:intergenic
GTTTGTGTTGGCTGAGCTAG+TGG 0.622781 1_3:-3146937 None:intergenic
TCTTCTTATCAAGCCCTCGG+TGG 0.636904 1_3:+3146828 Msa0097340:CDS
ATCACGTTGATGACTATGTG+TGG 0.647702 1_3:-3147111 None:intergenic
TGGAAGATTAGGTTCATCGA+AGG 0.659843 1_3:-3146610 None:intergenic
TGTGTTGGCTGAGCTAGTGG+TGG 0.672396 1_3:-3146934 None:intergenic
TTCATCGAAGGTGAATTTAG+GGG 0.676237 1_3:-3146598 None:intergenic
CACAAACGTTGTCACTACGA+AGG 0.683725 1_3:+3147032 Msa0097340:CDS
AGCTCAGCCAACACAAACGG+TGG 0.690830 1_3:+3146942 Msa0097340:CDS
TCAAAGGCTTGAAATCATGG+CGG 0.753429 1_3:-3146728 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! AAATTCGGAATTTCAATCTT+GGG - chr1_3:3147248-3147267 None:intergenic 25.0%
! AAAATTCGGAATTTCAATCT+TGG - chr1_3:3147249-3147268 None:intergenic 25.0%
AGAACATTTGTAACTGAGTT+TGG - chr1_3:3146790-3146809 None:intergenic 30.0%
AATTTAGGGGTAGTAGAAGT+GGG - chr1_3:3146588-3146607 None:intergenic 35.0%
TTCATCGAAGGTGAATTTAG+GGG - chr1_3:3146601-3146620 None:intergenic 35.0%
GTTCATCGAAGGTGAATTTA+GGG - chr1_3:3146602-3146621 None:intergenic 35.0%
GATTCAAAGGCTTGAAATCA+TGG - chr1_3:3146734-3146753 None:intergenic 35.0%
! TTGTTGTTGTCAATGGTTGT+TGG - chr1_3:3146762-3146781 None:intergenic 35.0%
! TTTTCTTCTTATCAAGCCCT+CGG + chr1_3:3146825-3146844 Msa0097340:CDS 35.0%
! ATGAGTGTTCGATTTGTCAT+AGG + chr1_3:3146979-3146998 Msa0097340:CDS 35.0%
TGATTTCGATCTGAATATCC+CGG + chr1_3:3147130-3147149 Msa0097340:CDS 35.0%
CCAATCTTATTAGCAAACTC+CGG - chr1_3:3147161-3147180 None:intergenic 35.0%
GAATTTAGGGGTAGTAGAAG+TGG - chr1_3:3146589-3146608 None:intergenic 40.0%
GGTTCATCGAAGGTGAATTT+AGG - chr1_3:3146603-3146622 None:intergenic 40.0%
TGGAAGATTAGGTTCATCGA+AGG - chr1_3:3146613-3146632 None:intergenic 40.0%
TCGATGAACCTAATCTTCCA+TGG + chr1_3:3146613-3146632 Msa0097340:CDS 40.0%
CGTTTAGTCCATGGAAGATT+AGG - chr1_3:3146624-3146643 None:intergenic 40.0%
GAACGTTTACGTTTAGTCCA+TGG - chr1_3:3146633-3146652 None:intergenic 40.0%
TCAAAGGCTTGAAATCATGG+CGG - chr1_3:3146731-3146750 None:intergenic 40.0%
TTGTTGTCAATGGTTGTTGG+TGG - chr1_3:3146759-3146778 None:intergenic 40.0%
!! GGTGTTGTTGTTGTTGTCAA+TGG - chr1_3:3146769-3146788 None:intergenic 40.0%
TCTGCTATAACTGTCTCTGA+AGG + chr1_3:3147080-3147099 Msa0097340:CDS 40.0%
! TATAACTGTCTCTGAAGGTG+TGG + chr1_3:3147085-3147104 Msa0097340:CDS 40.0%
! ATAACTGTCTCTGAAGGTGT+GGG + chr1_3:3147086-3147105 Msa0097340:CDS 40.0%
!! ATCACGTTGATGACTATGTG+TGG - chr1_3:3147114-3147133 None:intergenic 40.0%
!! CCGGAGTTTGCTAATAAGAT+TGG + chr1_3:3147158-3147177 Msa0097340:CDS 40.0%
TTCTTCATCATCACAGGATG+AGG - chr1_3:3147203-3147222 None:intergenic 40.0%
GCTTTCTTCTTCATCATCAC+AGG - chr1_3:3147209-3147228 None:intergenic 40.0%
!! GTTGTTGGTGGTGGATTCAA+AGG - chr1_3:3146747-3146766 None:intergenic 45.0%
! TTGTCAATGGTTGTTGGTGG+TGG - chr1_3:3146756-3146775 None:intergenic 45.0%
ACTAGCTCAGCCAACACAAA+CGG + chr1_3:3146939-3146958 Msa0097340:CDS 45.0%
TTTCCGACAGGACAAGCTTT+GGG + chr1_3:3147005-3147024 Msa0097340:CDS 45.0%
CACAAACGTTGTCACTACGA+AGG + chr1_3:3147032-3147051 Msa0097340:CDS 45.0%
!! TGTCACTACGAAGGTGTTGT+TGG + chr1_3:3147041-3147060 Msa0097340:CDS 45.0%
TCTGAATATCCCGGCTTATC+CGG + chr1_3:3147139-3147158 Msa0097340:CDS 45.0%
TTAGCAAACTCCGGATAAGC+CGG - chr1_3:3147152-3147171 None:intergenic 45.0%
! GAAGAAAGCTCGTGTTTTCG+TGG + chr1_3:3147220-3147239 Msa0097340:CDS 45.0%
! TGAAATCATGGCGGTTGGTG+TGG - chr1_3:3146722-3146741 None:intergenic 50.0%
AGGCTTGAAATCATGGCGGT+TGG - chr1_3:3146727-3146746 None:intergenic 50.0%
TCTTCTTATCAAGCCCTCGG+TGG + chr1_3:3146828-3146847 Msa0097340:CDS 50.0%
ACTTGCTTTGTGTCCACCGA+GGG - chr1_3:3146844-3146863 None:intergenic 50.0%
AGTCACCGCAAAAACTCCGT+CGG + chr1_3:3146861-3146880 Msa0097340:CDS 50.0%
!! GTTTGTGTTGGCTGAGCTAG+TGG - chr1_3:3146940-3146959 None:intergenic 50.0%
TGTCATAGGTCGTTTCCGAC+AGG + chr1_3:3146993-3147012 Msa0097340:CDS 50.0%
GTTTCCGACAGGACAAGCTT+TGG + chr1_3:3147004-3147023 Msa0097340:CDS 50.0%
!! CACTACGAAGGTGTTGTTGG+TGG + chr1_3:3147044-3147063 Msa0097340:CDS 50.0%
!! TACGAAGGTGTTGTTGGTGG+TGG + chr1_3:3147047-3147066 Msa0097340:CDS 50.0%
TAGCAAACTCCGGATAAGCC+GGG - chr1_3:3147151-3147170 None:intergenic 50.0%
TGTCTCATCATGCTCGCTCG+TGG + chr1_3:3146696-3146715 Msa0097340:CDS 55.0%
! GACTTGCTTTGTGTCCACCG+AGG - chr1_3:3146845-3146864 None:intergenic 55.0%
! TGGCAGCTGAGGAAGTTGGT+GGG - chr1_3:3146917-3146936 None:intergenic 55.0%
!! TGTGTTGGCTGAGCTAGTGG+TGG - chr1_3:3146937-3146956 None:intergenic 55.0%
AGCTCAGCCAACACAAACGG+TGG + chr1_3:3146942-3146961 Msa0097340:CDS 55.0%
TCAGCCAACACAAACGGTGG+CGG + chr1_3:3146945-3146964 Msa0097340:CDS 55.0%
AACACCGCCACCGTTTGTGT+TGG - chr1_3:3146952-3146971 None:intergenic 55.0%
CCACCCAAAGCTTGTCCTGT+CGG - chr1_3:3147011-3147030 None:intergenic 55.0%
CACCGCAAAAACTCCGTCGG+TGG + chr1_3:3146864-3146883 Msa0097340:CDS 60.0%
! CGCCACCGACGGAGTTTTTG+CGG - chr1_3:3146869-3146888 None:intergenic 60.0%
CGCAAAAACTCCGTCGGTGG+CGG + chr1_3:3146867-3146886 Msa0097340:CDS 60.0%
AACACCAACACCGCCACCGA+CGG - chr1_3:3146880-3146899 None:intergenic 60.0%
GTGGCAGCTGAGGAAGTTGG+TGG - chr1_3:3146918-3146937 None:intergenic 60.0%
GTGGTGGCAGCTGAGGAAGT+TGG - chr1_3:3146921-3146940 None:intergenic 60.0%
TGAGCTAGTGGTGGCAGCTG+AGG - chr1_3:3146928-3146947 None:intergenic 60.0%
!! CCGACAGGACAAGCTTTGGG+TGG + chr1_3:3147008-3147027 Msa0097340:CDS 60.0%
! AACTCCGTCGGTGGCGGTGT+TGG + chr1_3:3146873-3146892 Msa0097340:CDS 65.0%
!! GTCGGTGGCGGTGTTGGTGT+TGG + chr1_3:3146879-3146898 Msa0097340:CDS 65.0%
!! GGTGGCGGTGTTGGTGTTGG+TGG + chr1_3:3146882-3146901 Msa0097340:CDS 65.0%
Chromosome Type Strat End Strand Name
chr1_3 gene 3146561 3147274 3146561 ID=Msa0097340;Name=Msa0097340
chr1_3 mRNA 3146561 3147274 3146561 ID=Msa0097340-mRNA-1;Parent=Msa0097340;Name=Msa0097340-mRNA-1;_AED=0.01;_eAED=0.01;_QI=0|-1|0|1|-1|1|1|0|237
chr1_3 exon 3146561 3147274 3146561 ID=Msa0097340-mRNA-1:exon:882;Parent=Msa0097340-mRNA-1
chr1_3 CDS 3146561 3147274 3146561 ID=Msa0097340-mRNA-1:cds;Parent=Msa0097340-mRNA-1
Gene Sequence

>Msa0097340

ATGGCTCTTGAAGCACTTAACTCACCCACTTCTACTACCCCTAAATTCACCTTCGATGAACCTAATCTTCCATGGACTAAACGTAAACGTTCTAAACGTTCACGTTCATGCACTGAAGAAGAGTATCTTGCTCTTTGTCTCATCATGCTCGCTCGTGGCCACACCAACCGCCATGATTTCAAGCCTTTGAATCCACCACCAACAACCATTGACAACAACAACAACACCAAACTCAGTTACAAATGTTCTGTCTGTAACAAAGAGTTTTCTTCTTATCAAGCCCTCGGTGGACACAAAGCAAGTCACCGCAAAAACTCCGTCGGTGGCGGTGTTGGTGTTGGTGGTGATGATCACCCACCAACTTCCTCAGCTGCCACCACTAGCTCAGCCAACACAAACGGTGGCGGTGTTAGATCTCATGAGTGTTCGATTTGTCATAGGTCGTTTCCGACAGGACAAGCTTTGGGTGGACACAAACGTTGTCACTACGAAGGTGTTGTTGGTGGTGGTGCTTCTGCTTCTGCTATAACTGTCTCTGAAGGTGTGGGATCCACACATAGTCATCAACGTGATTTCGATCTGAATATCCCGGCTTATCCGGAGTTTGCTAATAAGATTGGAGAAGATGAAGTTGAAAGTCCTCATCCTGTGATGATGAAGAAGAAAGCTCGTGTTTTCGTGGTGCCCAAGATTGAAATTCCGAATTTTCAGTGA
Protein sequence

>Msa0097340

MALEALNSPTSTTPKFTFDEPNLPWTKRKRSKRSRSCTEEEYLALCLIMLARGHTNRHDFKPLNPPPTTIDNNNNTKLSYKCSVCNKEFSSYQALGGHKASHRKNSVGGGVGVGGDDHPPTSSAATTSSANTNGGGVRSHECSICHRSFPTGQALGGHKRCHYEGVVGGGASASAITVSEGVGSTHSHQRDFDLNIPAYPEFANKIGEDEVESPHPVMMKKKARVFVVPKIEIPNFQ*