AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0904930

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0904930 MtrunA17_Chr3g0145121 77.358 159 30 1 1 153 143 301 7.03e-73 220
Msa0904930 MtrunA17_Chr4g0035891 54.676 139 53 2 14 152 167 295 2.86e-40 137
Msa0904930 MtrunA17_Chr5g0404981 71.429 63 18 0 76 138 309 371 2.04e-27 105
Msa0904930 MtrunA17_Chr8g0372291 68.571 70 19 1 74 143 225 291 4.24e-27 102
Msa0904930 MtrunA17_Chr3g0140331 41.727 139 66 3 11 137 188 323 3.72e-25 98.6
Msa0904930 MtrunA17_Chr1g0169431 70.968 62 18 0 75 136 180 241 8.27e-25 95.5
Msa0904930 MtrunA17_Chr8g0340401 44.715 123 62 3 14 136 179 295 1.46e-24 96.7
Msa0904930 MtrunA17_Chr1g0199671 58.667 75 31 0 76 150 251 325 2.25e-24 96.3
Msa0904930 MtrunA17_Chr6g0461591 60.870 69 27 0 63 131 188 256 3.68e-23 91.7
Msa0904930 MtrunA17_Chr1g0146231 38.621 145 70 2 11 137 161 304 3.83e-23 93.2
Msa0904930 MtrunA17_Chr7g0253101 63.077 65 24 0 67 131 188 252 1.54e-22 90.1
Msa0904930 MtrunA17_Chr1g0213161 56.579 76 33 0 74 149 159 234 1.76e-22 89.4
Msa0904930 MtrunA17_Chr4g0028961 67.241 58 19 0 76 133 241 298 1.02e-21 89.0
Msa0904930 MtrunA17_Chr5g0395391 67.213 61 20 0 74 134 277 337 3.10e-21 87.8
Msa0904930 MtrunA17_Chr5g0395391 60.000 65 26 0 74 138 175 239 1.28e-18 80.9
Msa0904930 MtrunA17_Chr2g0326771 67.857 56 18 0 76 131 225 280 5.72e-21 86.7
Msa0904930 MtrunA17_Chr7g0232671 38.667 75 46 0 54 128 174 248 1.52e-12 63.2
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0904930 AT5G66320.2 51.818 110 47 2 31 134 207 316 1.48e-28 107
Msa0904930 AT5G66320.1 51.818 110 47 2 31 134 207 316 1.48e-28 107
Msa0904930 AT4G36240.1 45.455 121 55 3 21 134 115 231 5.21e-27 101
Msa0904930 AT3G60530.1 45.669 127 62 2 11 134 103 225 7.55e-26 98.6
Msa0904930 AT3G51080.1 71.667 60 17 0 75 134 229 288 9.20e-26 99.8
Msa0904930 AT4G32890.1 42.537 134 66 3 11 136 136 266 1.13e-24 97.1
Msa0904930 AT5G25830.1 50.943 106 43 2 39 136 184 288 1.52e-24 97.1
Msa0904930 AT3G24050.1 55.422 83 37 0 51 133 178 260 4.39e-24 94.7
Msa0904930 AT4G34680.1 42.222 135 69 2 8 142 129 254 2.19e-23 92.8
Msa0904930 AT4G34680.2 42.222 135 69 2 8 142 129 254 2.19e-23 92.8
Msa0904930 AT3G54810.1 69.492 59 18 0 76 134 238 296 1.87e-22 91.3
Msa0904930 AT3G54810.2 69.492 59 18 0 76 134 238 296 1.87e-22 91.3
Msa0904930 AT2G45050.1 57.746 71 30 0 67 137 179 249 4.61e-22 89.4
Msa0904930 AT1G08000.2 65.517 58 20 0 77 134 228 285 3.11e-20 85.1
Msa0904930 AT1G08000.1 65.517 58 20 0 77 134 228 285 3.11e-20 85.1
Msa0904930 AT1G08010.2 61.667 60 23 0 76 135 229 288 3.42e-20 84.7
Msa0904930 AT1G08010.1 61.667 60 23 0 76 135 229 288 3.42e-20 84.7
Msa0904930 AT1G08010.3 61.667 60 23 0 76 135 229 288 3.42e-20 84.7
Msa0904930 AT3G45170.1 53.333 60 28 0 75 134 123 182 1.81e-17 75.9
Msa0904930 AT2G28340.1 54.237 59 27 0 77 135 201 259 1.16e-16 75.1

Find 48 sgRNAs with CRISPR-Local

Find 58 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CGTTGTAATGACCCTCTTCT+TGG 0.263834 6_2:+2668476 None:intergenic
TCCTCATCTCCAACACTTTA+CGG 0.306611 6_2:+2668282 None:intergenic
CAACACTTTACGGTGGCTAT+TGG 0.312622 6_2:+2668292 None:intergenic
CTTAGCAAGTGGTAACCATT+TGG 0.353432 6_2:+2668213 None:intergenic
TCAGCTTGTAGCCCAACTTT+TGG 0.370479 6_2:-2668329 Msa0904930:CDS
CTTCGTAGTTCTGGTCTTTG+TGG 0.374826 6_2:+2668626 None:intergenic
TTAGCAAGTGGTAACCATTT+GGG 0.424230 6_2:+2668214 None:intergenic
TGGACCGGAACCCGGTTTAG+TGG 0.433007 6_2:-2668243 Msa0904930:CDS
TGAGTCCAAACGCTAGGGTT+GGG 0.434698 6_2:+2668594 None:intergenic
TGAGCCACTAAACCGGGTTC+CGG 0.434803 6_2:+2668239 None:intergenic
TGAATTTCACTGCCAAAAGT+TGG 0.437875 6_2:+2668317 None:intergenic
TTGGGTCTGAGCCACTAAAC+CGG 0.440417 6_2:+2668232 None:intergenic
GAAAACCCAACCCTAGCGTT+TGG 0.440713 6_2:-2668599 Msa0904930:CDS
GAATTTCACTGCCAAAAGTT+GGG 0.447151 6_2:+2668318 None:intergenic
AAGTCCGAGGTCCAAGTTGT+TGG 0.456727 6_2:-2668507 Msa0904930:CDS
AGTCCGAGGTCCAAGTTGTT+GGG 0.458770 6_2:-2668506 Msa0904930:CDS
AAGACGCCGCAGTGGAGAAC+CGG 0.467079 6_2:-2668428 Msa0904930:CDS
TGGAACTCAACCCAACAACT+TGG 0.469756 6_2:+2668496 None:intergenic
TTCTTCTGTTTCTTCGCTGG+TGG 0.490862 6_2:+2668531 None:intergenic
AACCCTACACGCGTTACAAA+GGG 0.494117 6_2:+2668388 None:intergenic
AAGTGTTGGAGATGAGGAAG+AGG 0.494772 6_2:-2668277 Msa0904930:CDS
AACCCTTTGTAACGCGTGTA+GGG 0.499250 6_2:-2668390 Msa0904930:CDS
GAGCGCTGAGTCCAAACGCT+AGG 0.511887 6_2:+2668588 None:intergenic
CAACCCAACAACTTGGACCT+CGG 0.512258 6_2:+2668503 None:intergenic
GCAGTGGAGAACCGGTCCGA+TGG 0.519611 6_2:-2668420 Msa0904930:CDS
TTGGAGATGAGGAAGAGGAA+AGG 0.523265 6_2:-2668272 Msa0904930:CDS
AAACCCTTTGTAACGCGTGT+AGG 0.525215 6_2:-2668391 Msa0904930:CDS
TGGGTCTGAGCCACTAAACC+GGG 0.528859 6_2:+2668233 None:intergenic
CTGAGTCCAAACGCTAGGGT+TGG 0.531575 6_2:+2668593 None:intergenic
TGTAGGGTTCAGTATAAATC+CGG 0.531937 6_2:-2668374 Msa0904930:CDS
TTTAGTGGCTCAGACCCAAA+TGG 0.544756 6_2:-2668228 Msa0904930:CDS
AGGAAGAGGAAAGGAATGGT+TGG 0.549859 6_2:-2668263 Msa0904930:CDS
CAGTGGAGAACCGGTCCGAT+GGG 0.550729 6_2:-2668419 Msa0904930:CDS
GGAATGGTTGGACCGGAACC+CGG 0.552734 6_2:-2668251 Msa0904930:CDS
GAGGAAAGGAATGGTTGGAC+CGG 0.555733 6_2:-2668258 Msa0904930:CDS
TGGGTTGAGTTCCAAGAAGA+GGG 0.556793 6_2:-2668487 Msa0904930:CDS
CAATAGCCACCGTAAAGTGT+TGG 0.557110 6_2:-2668291 Msa0904930:CDS
ACCGTAAAGTGTTGGAGATG+AGG 0.560291 6_2:-2668283 Msa0904930:CDS
GAACCCTACACGCGTTACAA+AGG 0.560340 6_2:+2668387 None:intergenic
TTGGGTTGAGTTCCAAGAAG+AGG 0.583060 6_2:-2668488 Msa0904930:CDS
GATGAGGAAGAGGAAAGGAA+TGG 0.588367 6_2:-2668267 Msa0904930:CDS
AGCGCTGAGTCCAAACGCTA+GGG 0.592846 6_2:+2668589 None:intergenic
TAATCTAATGACTTAGCAAG+TGG 0.603751 6_2:+2668202 None:intergenic
AGGCGCAGAAGACGCCGCAG+TGG 0.630481 6_2:-2668436 Msa0904930:CDS
GGGTTCAGTATAAATCCGGT+CGG 0.677319 6_2:-2668370 Msa0904930:CDS
TCATCTCCAACACTTTACGG+TGG 0.697799 6_2:+2668285 None:intergenic
ATCGGACCGGTTCTCCACTG+CGG 0.715648 6_2:+2668422 None:intergenic
GAAGAGGGTCATTACAACGA+CGG 0.718772 6_2:-2668472 Msa0904930:intron

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! TTTTCTATTCTTCGTAGTTC+TGG + chr6_2:2668269-2668288 None:intergenic 30.0%
!! TTTTTCTTCTGTTTCTTCGC+TGG + chr6_2:2668358-2668377 None:intergenic 35.0%
TGTAGGGTTCAGTATAAATC+CGG - chr6_2:2668509-2668528 Msa0904930:CDS 35.0%
GAATTTCACTGCCAAAAGTT+GGG + chr6_2:2668568-2668587 None:intergenic 35.0%
TGAATTTCACTGCCAAAAGT+TGG + chr6_2:2668569-2668588 None:intergenic 35.0%
TTAGCAAGTGGTAACCATTT+GGG + chr6_2:2668672-2668691 None:intergenic 35.0%
GAAACAGAAGAAAAAGTCCG+AGG - chr6_2:2668363-2668382 Msa0904930:CDS 40.0%
!! CAAAGGGTTTTAACACCCAT+CGG + chr6_2:2668482-2668501 None:intergenic 40.0%
! ATCCTTTGAAAAAAGCCGAC+CGG + chr6_2:2668531-2668550 None:intergenic 40.0%
TCCTCATCTCCAACACTTTA+CGG + chr6_2:2668604-2668623 None:intergenic 40.0%
!! CTTCGTAGTTCTGGTCTTTG+TGG + chr6_2:2668260-2668279 None:intergenic 45.0%
GGTGCACCAAAAACAACAGA+CGG + chr6_2:2668334-2668353 None:intergenic 45.0%
! TTCTTCTGTTTCTTCGCTGG+TGG + chr6_2:2668355-2668374 None:intergenic 45.0%
TGGAACTCAACCCAACAACT+TGG + chr6_2:2668390-2668409 None:intergenic 45.0%
!! TTGGGTTGAGTTCCAAGAAG+AGG - chr6_2:2668395-2668414 Msa0904930:CDS 45.0%
! TGGGTTGAGTTCCAAGAAGA+GGG - chr6_2:2668396-2668415 Msa0904930:CDS 45.0%
CGTTGTAATGACCCTCTTCT+TGG + chr6_2:2668410-2668429 None:intergenic 45.0%
GAAGAGGGTCATTACAACGA+CGG - chr6_2:2668411-2668430 Msa0904930:CDS 45.0%
AAACCCTTTGTAACGCGTGT+AGG - chr6_2:2668492-2668511 Msa0904930:CDS 45.0%
AACCCTTTGTAACGCGTGTA+GGG - chr6_2:2668493-2668512 Msa0904930:CDS 45.0%
AACCCTACACGCGTTACAAA+GGG + chr6_2:2668498-2668517 None:intergenic 45.0%
GGGTTCAGTATAAATCCGGT+CGG - chr6_2:2668513-2668532 Msa0904930:CDS 45.0%
!!! ATCCGGTCGGCTTTTTTCAA+AGG - chr6_2:2668526-2668545 Msa0904930:CDS 45.0%
! TCAGCTTGTAGCCCAACTTT+TGG - chr6_2:2668554-2668573 Msa0904930:CDS 45.0%
CAACACTTTACGGTGGCTAT+TGG + chr6_2:2668594-2668613 None:intergenic 45.0%
CAATAGCCACCGTAAAGTGT+TGG - chr6_2:2668592-2668611 Msa0904930:CDS 45.0%
TCATCTCCAACACTTTACGG+TGG + chr6_2:2668601-2668620 None:intergenic 45.0%
!! ACCGTAAAGTGTTGGAGATG+AGG - chr6_2:2668600-2668619 Msa0904930:CDS 45.0%
!! AAGTGTTGGAGATGAGGAAG+AGG - chr6_2:2668606-2668625 Msa0904930:CDS 45.0%
TTGGAGATGAGGAAGAGGAA+AGG - chr6_2:2668611-2668630 Msa0904930:CDS 45.0%
GATGAGGAAGAGGAAAGGAA+TGG - chr6_2:2668616-2668635 Msa0904930:CDS 45.0%
AGGAAGAGGAAAGGAATGGT+TGG - chr6_2:2668620-2668639 Msa0904930:CDS 45.0%
TTTAGTGGCTCAGACCCAAA+TGG - chr6_2:2668655-2668674 Msa0904930:CDS 45.0%
GAAAACCCAACCCTAGCGTT+TGG - chr6_2:2668284-2668303 Msa0904930:CDS 50.0%
TGAGTCCAAACGCTAGGGTT+GGG + chr6_2:2668292-2668311 None:intergenic 50.0%
!!! GGACTCAGCGCTCGTTTTTT+CGG - chr6_2:2668305-2668324 Msa0904930:CDS 50.0%
!!! CGGTCACCGTCTGTTGTTTT+TGG - chr6_2:2668325-2668344 Msa0904930:CDS 50.0%
AAGTCCGAGGTCCAAGTTGT+TGG - chr6_2:2668376-2668395 Msa0904930:CDS 50.0%
AGTCCGAGGTCCAAGTTGTT+GGG - chr6_2:2668377-2668396 Msa0904930:CDS 50.0%
CAACCCAACAACTTGGACCT+CGG + chr6_2:2668383-2668402 None:intergenic 50.0%
!! GGTTTTAACACCCATCGGAC+CGG + chr6_2:2668477-2668496 None:intergenic 50.0%
GAACCCTACACGCGTTACAA+AGG + chr6_2:2668499-2668518 None:intergenic 50.0%
GAGGAAAGGAATGGTTGGAC+CGG - chr6_2:2668625-2668644 Msa0904930:CDS 50.0%
TTGGGTCTGAGCCACTAAAC+CGG + chr6_2:2668654-2668673 None:intergenic 50.0%
CTGAGTCCAAACGCTAGGGT+TGG + chr6_2:2668293-2668312 None:intergenic 55.0%
! AGCGCTGAGTCCAAACGCTA+GGG + chr6_2:2668297-2668316 None:intergenic 55.0%
ACGACGGTGTAGTCATTGCC+AGG - chr6_2:2668427-2668446 Msa0904930:CDS 55.0%
TGAGCCACTAAACCGGGTTC+CGG + chr6_2:2668647-2668666 None:intergenic 55.0%
TGGGTCTGAGCCACTAAACC+GGG + chr6_2:2668653-2668672 None:intergenic 55.0%
!! GAGCGCTGAGTCCAAACGCT+AGG + chr6_2:2668298-2668317 None:intergenic 60.0%
AAGACGCCGCAGTGGAGAAC+CGG - chr6_2:2668455-2668474 Msa0904930:intron 60.0%
! ATCGGACCGGTTCTCCACTG+CGG + chr6_2:2668464-2668483 None:intergenic 60.0%
CAGTGGAGAACCGGTCCGAT+GGG - chr6_2:2668464-2668483 Msa0904930:intron 60.0%
GGAATGGTTGGACCGGAACC+CGG - chr6_2:2668632-2668651 Msa0904930:CDS 60.0%
TGGACCGGAACCCGGTTTAG+TGG - chr6_2:2668640-2668659 Msa0904930:CDS 60.0%
GCAGTGGAGAACCGGTCCGA+TGG - chr6_2:2668463-2668482 Msa0904930:intron 65.0%
ACTGCGGCGTCTTCTGCGCC+TGG + chr6_2:2668448-2668467 None:intergenic 70.0%
AGGCGCAGAAGACGCCGCAG+TGG - chr6_2:2668447-2668466 Msa0904930:intron 70.0%
Chromosome Type Strat End Strand Name
chr6_2 gene 2668214 2668691 2668214 ID=Msa0904930;Name=Msa0904930
chr6_2 mRNA 2668214 2668691 2668214 ID=Msa0904930-mRNA-1;Parent=Msa0904930;Name=Msa0904930-mRNA-1;_AED=0.09;_eAED=0.16;_QI=0|0|0|1|0|0|2|0|153
chr6_2 exon 2668473 2668691 2668473 ID=Msa0904930-mRNA-1:exon:892;Parent=Msa0904930-mRNA-1
chr6_2 exon 2668214 2668456 2668214 ID=Msa0904930-mRNA-1:exon:891;Parent=Msa0904930-mRNA-1
chr6_2 CDS 2668473 2668691 2668473 ID=Msa0904930-mRNA-1:cds;Parent=Msa0904930-mRNA-1
chr6_2 CDS 2668214 2668456 2668214 ID=Msa0904930-mRNA-1:cds;Parent=Msa0904930-mRNA-1
Gene Sequence

>Msa0904930

CATGGAAAATCTTTTCGTTTTTCAACTGAAAAAATAAAAATTACCACAAAGACCAGAACTACGAAGAATAGAAAACCCAACCCTAGCGTTTGGACTCAGCGCTCGTTTTTTCGGTCACCGTCTGTTGTTTTTGGTGCACCACCAGCGAAGAAACAGAAGAAAAAGTCCGAGGTCCAAGTTGTTGGGTTGAGTTCCAAGAAGAGGGTCATTACAACGACGGCGCAGAAGACGCCGCAGTGGAGAACCGGTCCGATGGGTGTTAAAACCCTTTGTAACGCGTGTAGGGTTCAGTATAAATCCGGTCGGCTTTTTTCAAAGGATAGATCAGCTTGTAGCCCAACTTTTGGCAGTGAAATTCATTCCAATAGCCACCGTAAAGTGTTGGAGATGAGGAAGAGGAAAGGAATGGTTGGACCGGAACCCGGTTTAGTGGCTCAGACCCAAATGGTTACCACTTGCTAA
Protein sequence

>Msa0904930

HGKSFRFSTEKIKITTKTRTTKNRKPNPSVWTQRSFFRSPSVVFGAPPAKKQKKKSEVQVVGLSSKKRVITTTAQKTPQWRTGPMGVKTLCNACRVQYKSGRLFSKDRSACSPTFGSEIHSNSHRKVLEMRKRKGMVGPEPGLVAQTQMVTTC*