AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1326740


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1326740 MtrunA17_Chr8g0385281 80.147 136 6 1 1 115 181 316 1.12e-72 219
Msa1326740 MtrunA17_Chr3g0131061 71.852 135 17 1 1 114 180 314 6.86e-66 202
Msa1326740 MtrunA17_Chr2g0277501 63.704 135 28 1 1 114 180 314 7.18e-57 179
Msa1326740 MtrunA17_Chr5g0399911 52.419 124 37 2 1 102 195 318 2.70e-36 126
Msa1326740 MtrunA17_Chr4g0055451 50.000 136 42 3 1 113 181 313 6.93e-36 125
Msa1326740 MtrunA17_Chr8g0381821 48.333 120 39 2 1 99 180 297 7.45e-32 114
Msa1326740 MtrunA17_Chr5g0426521 49.593 123 38 2 1 102 180 299 7.61e-32 114
Msa1326740 MtrunA17_Chr4g0055431 50.407 123 35 3 1 100 187 306 9.33e-32 114
Msa1326740 MtrunA17_Chr4g0045371 48.780 123 41 2 1 102 199 320 2.91e-31 113
Msa1326740 MtrunA17_Chr3g0123791 46.400 125 44 2 1 102 181 305 3.07e-31 112
Msa1326740 MtrunA17_Chr8g0380661 44.882 127 49 1 1 106 177 303 1.40e-30 110
Msa1326740 MtrunA17_Chr1g0162301 47.967 123 42 2 1 102 200 321 1.87e-30 111
Msa1326740 MtrunA17_Chr5g0402661 44.715 123 46 2 1 102 194 315 5.00e-29 107
Msa1326740 MtrunA17_Chr8g0374571 44.715 123 46 2 1 102 199 320 7.25e-28 104
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1326740 AT1G10940.2 65.385 130 24 1 1 109 188 317 7.51e-57 180
Msa1326740 AT1G10940.1 65.385 130 24 1 1 109 180 309 8.16e-57 180
Msa1326740 AT1G60940.1 64.444 135 27 1 1 114 180 314 1.21e-56 179
Msa1326740 AT1G60940.2 64.444 135 27 1 1 114 180 314 1.21e-56 179
Msa1326740 AT5G63650.1 67.424 132 22 1 2 112 181 312 4.49e-56 177
Msa1326740 AT5G08590.2 65.414 133 24 2 2 113 105 236 5.35e-54 170
Msa1326740 AT5G08590.1 65.414 133 24 2 2 113 181 312 2.78e-53 170
Msa1326740 AT2G23030.1 61.194 134 29 2 3 113 182 315 1.25e-46 153
Msa1326740 AT4G33950.2 47.619 126 40 3 1 103 197 319 2.58e-31 113
Msa1326740 AT4G33950.1 44.444 135 49 3 1 112 197 328 3.99e-31 113
Msa1326740 AT1G78290.3 48.031 127 39 3 1 106 180 300 5.11e-29 107
Msa1326740 AT1G78290.2 48.031 127 39 3 1 106 180 300 5.11e-29 107
Msa1326740 AT5G66880.1 44.776 134 50 3 1 112 198 329 2.36e-28 105
Msa1326740 AT5G66880.2 44.776 134 50 3 1 112 198 329 2.36e-28 105
Msa1326740 AT3G50500.1 44.030 134 51 3 1 112 199 330 3.14e-28 105
Msa1326740 AT3G50500.2 43.609 133 53 2 1 112 206 337 3.59e-28 105
Msa1326740 AT4G40010.1 74.194 62 16 0 1 62 180 241 2.02e-27 103

Find 31 sgRNAs with CRISPR-Local

Find 120 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TGAGATATGTGAACATAATC+AGG 0.310733 8_4:+41352233 None:intergenic
TCTAGGCCGGTCAAAGGTTT+TGG 0.324015 8_4:-41351665 Msa1326740:CDS
CTCCAACTAGCATGACATAA+AGG 0.336939 8_4:+41352428 None:intergenic
AAAAGCTTGGGTTGCCTCTC+TGG 0.343755 8_4:+41351750 None:intergenic
CACTTTGAATAGAAAAGCTT+GGG 0.403772 8_4:+41351738 None:intergenic
GAGAACCTCCTCCGGTATCT+AGG 0.405420 8_4:-41351682 Msa1326740:CDS
AGCATATCCCTTTGAGGATC+GGG 0.410059 8_4:-41352407 Msa1326740:CDS
ACCCTTTATGTCATGCTAGT+TGG 0.433752 8_4:-41352430 Msa1326740:CDS
GCTGATTCAATTAGCTCCCT+TGG 0.435549 8_4:+41351788 None:intergenic
ACACTTTGAATAGAAAAGCT+TGG 0.460081 8_4:+41351737 None:intergenic
TAGCAACAAATATACGAGAT+AGG 0.461711 8_4:+41352195 None:intergenic
GACATAAAGGGTCACTCCAC+AGG 0.502214 8_4:+41352441 None:intergenic
TCCAACTAGCATGACATAAA+GGG 0.508696 8_4:+41352429 None:intergenic
CCTTTGACCGGCCTAGATAC+CGG 0.512013 8_4:+41351671 None:intergenic
GAGCATATCCCTTTGAGGAT+CGG 0.523974 8_4:-41352408 Msa1326740:CDS
GATAATGAAAATTGTGGGAG+AGG 0.536919 8_4:-41351708 Msa1326740:CDS
AGTTGGAGCATATCCCTTTG+AGG 0.541202 8_4:-41352413 Msa1326740:CDS
GGACGAGATAATGAAAATTG+TGG 0.541311 8_4:-41351714 Msa1326740:CDS
TCCCAGCCAAAACCTTTGAC+CGG 0.541467 8_4:+41351659 None:intergenic
AGGGTCATCCCGATCCTCAA+AGG 0.547475 8_4:+41352399 None:intergenic
ACCTCCTCCGGTATCTAGGC+CGG 0.548787 8_4:-41351678 Msa1326740:CDS
GACGAGATAATGAAAATTGT+GGG 0.549780 8_4:-41351713 Msa1326740:CDS
GGGTCATCCCGATCCTCAAA+GGG 0.551772 8_4:+41352400 None:intergenic
CCGGTATCTAGGCCGGTCAA+AGG 0.553923 8_4:-41351671 Msa1326740:CDS
ACCGGCCTAGATACCGGAGG+AGG 0.562102 8_4:+41351677 None:intergenic
TTGGCTGATGTGTGGTCCTG+TGG 0.571735 8_4:-41352457 Msa1326740:CDS
AGAGGCAAGAGAACCTCCTC+CGG 0.578941 8_4:-41351690 Msa1326740:CDS
GAGATATGTGAACATAATCA+GGG 0.595221 8_4:+41352234 None:intergenic
CAACAAATATACGAGATAGG+AGG 0.614585 8_4:+41352198 None:intergenic
CAAGCTGCATATTACCAGAG+AGG 0.690799 8_4:-41351764 Msa1326740:CDS
TTGACCGGCCTAGATACCGG+AGG 0.733082 8_4:+41351674 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTGTTTTCATAAAATTTCTA+GGG + chr8_4:41351738-41351757 None:intergenic 15.0%
!!! ATTGTTTTCATAAAATTTCT+AGG + chr8_4:41351739-41351758 None:intergenic 15.0%
!!! TTGTTTTCATAAAATTTCTA+GGG + chr8_4:41351738-41351757 None:intergenic 15.0%
!!! ATTGTTTTCATAAAATTTCT+AGG + chr8_4:41351739-41351758 None:intergenic 15.0%
!!! AAATTTTATGAAAACAATCC+AGG - chr8_4:41351741-41351760 Msa1326740:CDS 20.0%
!!! ATTTTTCTATTGTTACAGTA+TGG - chr8_4:41351984-41352003 Msa1326740:intron 20.0%
!!! AAATTTTATGAAAACAATCC+AGG - chr8_4:41351741-41351760 Msa1326740:CDS 20.0%
!!! ATTTTTCTATTGTTACAGTA+TGG - chr8_4:41351984-41352003 Msa1326740:intron 20.0%
!! TATTTGTTGCTAATCCATTA+AGG - chr8_4:41351931-41351950 Msa1326740:intron 25.0%
!! ATTTGTTGCTAATCCATTAA+GGG - chr8_4:41351932-41351951 Msa1326740:intron 25.0%
! ATCTATTAGGATTGACTAAT+TGG + chr8_4:41352202-41352221 None:intergenic 25.0%
! ATGGCGAAAATAATAAGTTT+GGG + chr8_4:41352247-41352266 None:intergenic 25.0%
! AATGGCGAAAATAATAAGTT+TGG + chr8_4:41352248-41352267 None:intergenic 25.0%
!! GGAAGATTCTTTAAAAACTA+TGG + chr8_4:41352309-41352328 None:intergenic 25.0%
!!! AGTTTTTAAAGAATCTTCCA+AGG - chr8_4:41352310-41352329 Msa1326740:intron 25.0%
!!! GTTTTTAAAGAATCTTCCAA+GGG - chr8_4:41352311-41352330 Msa1326740:intron 25.0%
!! TATTTGTTGCTAATCCATTA+AGG - chr8_4:41351931-41351950 Msa1326740:intron 25.0%
!! ATTTGTTGCTAATCCATTAA+GGG - chr8_4:41351932-41351951 Msa1326740:intron 25.0%
! ATCTATTAGGATTGACTAAT+TGG + chr8_4:41352202-41352221 None:intergenic 25.0%
! ATGGCGAAAATAATAAGTTT+GGG + chr8_4:41352247-41352266 None:intergenic 25.0%
! AATGGCGAAAATAATAAGTT+TGG + chr8_4:41352248-41352267 None:intergenic 25.0%
!! GGAAGATTCTTTAAAAACTA+TGG + chr8_4:41352309-41352328 None:intergenic 25.0%
!!! AGTTTTTAAAGAATCTTCCA+AGG - chr8_4:41352310-41352329 Msa1326740:intron 25.0%
!!! GTTTTTAAAGAATCTTCCAA+GGG - chr8_4:41352311-41352330 Msa1326740:intron 25.0%
CTGCAAAAGAAGATATGAAA+TGG + chr8_4:41351835-41351854 None:intergenic 30.0%
GAGATATGTGAACATAATCA+GGG + chr8_4:41351884-41351903 None:intergenic 30.0%
TGAGATATGTGAACATAATC+AGG + chr8_4:41351885-41351904 None:intergenic 30.0%
TAGCAACAAATATACGAGAT+AGG + chr8_4:41351923-41351942 None:intergenic 30.0%
TCATCAAAACATACCCTTAA+TGG + chr8_4:41351948-41351967 None:intergenic 30.0%
! ACTGTTTTCATAAGCTATCT+TGG - chr8_4:41352072-41352091 Msa1326740:intron 30.0%
TAAGAACTTGTGAGATTGTT+TGG + chr8_4:41352163-41352182 None:intergenic 30.0%
AACAATCTCACAAGTTCTTA+CGG - chr8_4:41352163-41352182 Msa1326740:intron 30.0%
CGATAAACAATGGATCTATT+AGG + chr8_4:41352215-41352234 None:intergenic 30.0%
CACTTTGAATAGAAAAGCTT+GGG + chr8_4:41352380-41352399 None:intergenic 30.0%
ACACTTTGAATAGAAAAGCT+TGG + chr8_4:41352381-41352400 None:intergenic 30.0%
! AAGCTTTTCTATTCAAAGTG+TGG - chr8_4:41352380-41352399 Msa1326740:CDS 30.0%
GACGAGATAATGAAAATTGT+GGG - chr8_4:41352402-41352421 Msa1326740:CDS 30.0%
CTGCAAAAGAAGATATGAAA+TGG + chr8_4:41351835-41351854 None:intergenic 30.0%
GAGATATGTGAACATAATCA+GGG + chr8_4:41351884-41351903 None:intergenic 30.0%
TGAGATATGTGAACATAATC+AGG + chr8_4:41351885-41351904 None:intergenic 30.0%
TAGCAACAAATATACGAGAT+AGG + chr8_4:41351923-41351942 None:intergenic 30.0%
TCATCAAAACATACCCTTAA+TGG + chr8_4:41351948-41351967 None:intergenic 30.0%
! ACTGTTTTCATAAGCTATCT+TGG - chr8_4:41352072-41352091 Msa1326740:intron 30.0%
TAAGAACTTGTGAGATTGTT+TGG + chr8_4:41352163-41352182 None:intergenic 30.0%
AACAATCTCACAAGTTCTTA+CGG - chr8_4:41352163-41352182 Msa1326740:intron 30.0%
CGATAAACAATGGATCTATT+AGG + chr8_4:41352215-41352234 None:intergenic 30.0%
CACTTTGAATAGAAAAGCTT+GGG + chr8_4:41352380-41352399 None:intergenic 30.0%
ACACTTTGAATAGAAAAGCT+TGG + chr8_4:41352381-41352400 None:intergenic 30.0%
! AAGCTTTTCTATTCAAAGTG+TGG - chr8_4:41352380-41352399 Msa1326740:CDS 30.0%
GACGAGATAATGAAAATTGT+GGG - chr8_4:41352402-41352421 Msa1326740:CDS 30.0%
TCCAACTAGCATGACATAAA+GGG + chr8_4:41351689-41351708 None:intergenic 35.0%
TGTATGAGATGTAACATACC+TGG + chr8_4:41351762-41351781 None:intergenic 35.0%
! TCTTCTTTTGCAGCTCATAA+TGG - chr8_4:41351842-41351861 Msa1326740:intron 35.0%
CAACAAATATACGAGATAGG+AGG + chr8_4:41351920-41351939 None:intergenic 35.0%
ATACGTTATTGTGTCATCTC+TGG - chr8_4:41352007-41352026 Msa1326740:intron 35.0%
AACAAGCTGAAAACCGTTTA+AGG - chr8_4:41352107-41352126 Msa1326740:intron 35.0%
GCTTATGACATGTCCTTAAA+CGG + chr8_4:41352123-41352142 None:intergenic 35.0%
GTAGTTAGCTCGATAAACAA+TGG + chr8_4:41352225-41352244 None:intergenic 35.0%
GGACGAGATAATGAAAATTG+TGG - chr8_4:41352401-41352420 Msa1326740:CDS 35.0%
GATAATGAAAATTGTGGGAG+AGG - chr8_4:41352407-41352426 Msa1326740:CDS 35.0%
TCCAACTAGCATGACATAAA+GGG + chr8_4:41351689-41351708 None:intergenic 35.0%
TGTATGAGATGTAACATACC+TGG + chr8_4:41351762-41351781 None:intergenic 35.0%
! TCTTCTTTTGCAGCTCATAA+TGG - chr8_4:41351842-41351861 Msa1326740:intron 35.0%
CAACAAATATACGAGATAGG+AGG + chr8_4:41351920-41351939 None:intergenic 35.0%
ATACGTTATTGTGTCATCTC+TGG - chr8_4:41352007-41352026 Msa1326740:intron 35.0%
AACAAGCTGAAAACCGTTTA+AGG - chr8_4:41352107-41352126 Msa1326740:intron 35.0%
GCTTATGACATGTCCTTAAA+CGG + chr8_4:41352123-41352142 None:intergenic 35.0%
GTAGTTAGCTCGATAAACAA+TGG + chr8_4:41352225-41352244 None:intergenic 35.0%
GGACGAGATAATGAAAATTG+TGG - chr8_4:41352401-41352420 Msa1326740:CDS 35.0%
GATAATGAAAATTGTGGGAG+AGG - chr8_4:41352407-41352426 Msa1326740:CDS 35.0%
ACCCTTTATGTCATGCTAGT+TGG - chr8_4:41351685-41351704 Msa1326740:CDS 40.0%
CTCCAACTAGCATGACATAA+AGG + chr8_4:41351690-41351709 None:intergenic 40.0%
! GAGAAATTCTGTGTCGACAA+TGG + chr8_4:41352266-41352285 None:intergenic 40.0%
TCGACACAGAATTTCTCTCA+AGG - chr8_4:41352269-41352288 Msa1326740:intron 40.0%
ACCCTTTATGTCATGCTAGT+TGG - chr8_4:41351685-41351704 Msa1326740:CDS 40.0%
CTCCAACTAGCATGACATAA+AGG + chr8_4:41351690-41351709 None:intergenic 40.0%
! GAGAAATTCTGTGTCGACAA+TGG + chr8_4:41352266-41352285 None:intergenic 40.0%
TCGACACAGAATTTCTCTCA+AGG - chr8_4:41352269-41352288 Msa1326740:intron 40.0%
AGTTGGAGCATATCCCTTTG+AGG - chr8_4:41351702-41351721 Msa1326740:CDS 45.0%
! GAGCATATCCCTTTGAGGAT+CGG - chr8_4:41351707-41351726 Msa1326740:CDS 45.0%
! AGCATATCCCTTTGAGGATC+GGG - chr8_4:41351708-41351727 Msa1326740:CDS 45.0%
! GCTGATTCAATTAGCTCCCT+TGG + chr8_4:41352330-41352349 None:intergenic 45.0%
CAAGCTGCATATTACCAGAG+AGG - chr8_4:41352351-41352370 Msa1326740:intron 45.0%
AGTTGGAGCATATCCCTTTG+AGG - chr8_4:41351702-41351721 Msa1326740:CDS 45.0%
! GAGCATATCCCTTTGAGGAT+CGG - chr8_4:41351707-41351726 Msa1326740:CDS 45.0%
! AGCATATCCCTTTGAGGATC+GGG - chr8_4:41351708-41351727 Msa1326740:CDS 45.0%
! GCTGATTCAATTAGCTCCCT+TGG + chr8_4:41352330-41352349 None:intergenic 45.0%
CAAGCTGCATATTACCAGAG+AGG - chr8_4:41352351-41352370 Msa1326740:intron 45.0%
GACATAAAGGGTCACTCCAC+AGG + chr8_4:41351677-41351696 None:intergenic 50.0%
! AAAAGCTTGGGTTGCCTCTC+TGG + chr8_4:41352368-41352387 None:intergenic 50.0%
! TCTAGGCCGGTCAAAGGTTT+TGG - chr8_4:41352450-41352469 Msa1326740:CDS 50.0%
TCCCAGCCAAAACCTTTGAC+CGG + chr8_4:41352459-41352478 None:intergenic 50.0%
GACATAAAGGGTCACTCCAC+AGG + chr8_4:41351677-41351696 None:intergenic 50.0%
! AAAAGCTTGGGTTGCCTCTC+TGG + chr8_4:41352368-41352387 None:intergenic 50.0%
! TCTAGGCCGGTCAAAGGTTT+TGG - chr8_4:41352450-41352469 Msa1326740:CDS 50.0%
TCCCAGCCAAAACCTTTGAC+CGG + chr8_4:41352459-41352478 None:intergenic 50.0%
TTGGCTGATGTGTGGTCCTG+TGG - chr8_4:41351658-41351677 Msa1326740:CDS 55.0%
GGGTCATCCCGATCCTCAAA+GGG + chr8_4:41351718-41351737 None:intergenic 55.0%
AGGGTCATCCCGATCCTCAA+AGG + chr8_4:41351719-41351738 None:intergenic 55.0%
AGAGGCAAGAGAACCTCCTC+CGG - chr8_4:41352425-41352444 Msa1326740:CDS 55.0%
GAGAACCTCCTCCGGTATCT+AGG - chr8_4:41352433-41352452 Msa1326740:CDS 55.0%
CCTTTGACCGGCCTAGATAC+CGG + chr8_4:41352447-41352466 None:intergenic 55.0%
!!! GCCGGTCAAAGGTTTTGGCT+GGG - chr8_4:41352455-41352474 Msa1326740:CDS 55.0%
TTGGCTGATGTGTGGTCCTG+TGG - chr8_4:41351658-41351677 Msa1326740:CDS 55.0%
GGGTCATCCCGATCCTCAAA+GGG + chr8_4:41351718-41351737 None:intergenic 55.0%
AGGGTCATCCCGATCCTCAA+AGG + chr8_4:41351719-41351738 None:intergenic 55.0%
AGAGGCAAGAGAACCTCCTC+CGG - chr8_4:41352425-41352444 Msa1326740:CDS 55.0%
GAGAACCTCCTCCGGTATCT+AGG - chr8_4:41352433-41352452 Msa1326740:CDS 55.0%
CCTTTGACCGGCCTAGATAC+CGG + chr8_4:41352447-41352466 None:intergenic 55.0%
!!! GCCGGTCAAAGGTTTTGGCT+GGG - chr8_4:41352455-41352474 Msa1326740:CDS 55.0%
ACCTCCTCCGGTATCTAGGC+CGG - chr8_4:41352437-41352456 Msa1326740:CDS 60.0%
TTGACCGGCCTAGATACCGG+AGG + chr8_4:41352444-41352463 None:intergenic 60.0%
CCGGTATCTAGGCCGGTCAA+AGG - chr8_4:41352444-41352463 Msa1326740:CDS 60.0%
!! GGCCGGTCAAAGGTTTTGGC+TGG - chr8_4:41352454-41352473 Msa1326740:CDS 60.0%
ACCTCCTCCGGTATCTAGGC+CGG - chr8_4:41352437-41352456 Msa1326740:CDS 60.0%
TTGACCGGCCTAGATACCGG+AGG + chr8_4:41352444-41352463 None:intergenic 60.0%
CCGGTATCTAGGCCGGTCAA+AGG - chr8_4:41352444-41352463 Msa1326740:CDS 60.0%
!! GGCCGGTCAAAGGTTTTGGC+TGG - chr8_4:41352454-41352473 Msa1326740:CDS 60.0%
ACCGGCCTAGATACCGGAGG+AGG + chr8_4:41352441-41352460 None:intergenic 65.0%
ACCGGCCTAGATACCGGAGG+AGG + chr8_4:41352441-41352460 None:intergenic 65.0%
Chromosome Type Strat End Strand Name
chr8_4 gene 41351658 41352479 41351658 ID=Msa1326740;Name=Msa1326740
chr8_4 mRNA 41351658 41352479 41351658 ID=Msa1326740-mRNA-1;Parent=Msa1326740;Name=Msa1326740-mRNA-1;_AED=0.10;_eAED=0.10;_QI=0|0|0|1|0.5|0.66|3|0|115
chr8_4 exon 41352375 41352479 41352375 ID=Msa1326740-mRNA-1:exon:12161;Parent=Msa1326740-mRNA-1
chr8_4 exon 41352202 41352282 41352202 ID=Msa1326740-mRNA-1:exon:12160;Parent=Msa1326740-mRNA-1
chr8_4 exon 41351658 41351816 41351658 ID=Msa1326740-mRNA-1:exon:12159;Parent=Msa1326740-mRNA-1
chr8_4 CDS 41352375 41352479 41352375 ID=Msa1326740-mRNA-1:cds;Parent=Msa1326740-mRNA-1
chr8_4 CDS 41352202 41352282 41352202 ID=Msa1326740-mRNA-1:cds;Parent=Msa1326740-mRNA-1
chr8_4 CDS 41351658 41351816 41351658 ID=Msa1326740-mRNA-1:cds;Parent=Msa1326740-mRNA-1
Gene Sequence

>Msa1326740

TTGGCTGATGTGTGGTCCTGTGGAGTGACCCTTTATGTCATGCTAGTTGGAGCATATCCCTTTGAGGATCGGGATGACCCTAGAAATTTTATGAAAACAATCCAGCTCATAATGGCTCTTCAATACAAAATCCCTGATTATGTTCACATATCTCAAGATTGCAAAAGCCTCCTATCTCGTATATTTAATCTTCCAAGGGAGCTAATTGAATCAGCTCAAGCTGCATATTACCAGAGAGGCAACCCAAGCTTTTCTATTCAAAGTGTGGACGAGATAATGAAAATTGTGGGAGAGGCAAGAGAACCTCCTCCGGTATCTAGGCCGGTCAAAGGTTTTGGCTGGGAA

Protein sequence

>Msa1326740

LADVWSCGVTLYVMLVGAYPFEDRDDPRNFMKTIQLIMALQYKIPDYVHISQDCKSLLSRIFNLPRELIESAQAAYYQRGNPSFSIQSVDEIMKIVGEAREPPPVSRPVKGFGWE