AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1204460

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1204460 MtrunA17_Chr4g0053571 74.477 239 56 4 3 239 78 313 2.07e-112 342
Msa1204460 MtrunA17_Chr4g0053521 73.029 241 64 1 1 241 76 315 5.26e-109 342
Msa1204460 MtrunA17_Chr4g0053521 72.269 238 62 3 3 239 634 868 3.21e-104 329
Msa1204460 MtrunA17_Chr4g0053561 69.027 226 69 1 3 228 76 300 2.79e-97 300
Msa1204460 MtrunA17_Chr4g0053601 68.794 141 43 1 101 241 1 140 1.75e-64 197
Msa1204460 MtrunA17_Chr4g0061081 36.179 246 129 6 6 241 95 322 2.09e-32 124
Msa1204460 MtrunA17_Chr1g0202711 32.787 244 143 7 4 241 95 323 5.37e-31 120
Msa1204460 MtrunA17_Chr8g0361611 33.333 240 137 4 3 241 82 299 1.02e-28 114
Msa1204460 MtrunA17_Chr4g0030441 34.156 243 139 6 3 241 84 309 5.14e-28 112
Msa1204460 MtrunA17_Chr7g0248161 32.271 251 138 9 4 241 75 306 9.23e-28 110
Msa1204460 MtrunA17_Chr2g0327671 38.785 214 112 6 3 215 83 278 1.58e-27 110
Msa1204460 MtrunA17_Chr6g0468691 34.400 250 138 9 3 241 77 311 3.17e-27 109
Msa1204460 MtrunA17_Chr8g0352381 31.429 245 151 6 1 241 108 339 1.12e-25 105
Msa1204460 MtrunA17_Chr2g0318301 31.535 241 145 6 5 241 81 305 6.17e-24 100
Msa1204460 MtrunA17_Chr4g0053611 82.456 57 10 0 6 62 84 140 1.07e-23 92.8
Msa1204460 MtrunA17_Chr1g0190581 32.645 242 134 10 6 234 78 303 3.93e-21 92.0
Msa1204460 MtrunA17_Chr7g0274261 30.924 249 142 9 6 241 89 320 1.67e-20 90.1
Msa1204460 MtrunA17_Chr2g0292501 28.462 260 141 9 5 241 81 318 4.17e-19 85.9
Msa1204460 MtrunA17_Chr5g0420151 32.743 226 124 10 1 214 85 294 2.35e-17 80.9
Msa1204460 MtrunA17_Chr7g0245131 29.876 241 140 10 1 229 77 300 3.66e-17 80.5
Msa1204460 MtrunA17_Chr7g0219781 27.559 254 157 10 6 241 92 336 1.94e-11 63.5
Msa1204460 MtrunA17_Chr1g0165521 27.419 248 128 11 3 241 82 286 3.20e-11 62.8
Msa1204460 MtrunA17_Chr7g0219671 26.482 253 164 9 6 241 90 337 3.59e-11 62.8
Msa1204460 MtrunA17_Chr7g0219591 27.273 253 157 12 6 241 91 333 3.76e-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
Msa1204460 AT4G00300.1 31.250 240 150 6 5 241 80 307 2.57e-29 114
Msa1204460 AT2G23200.1 34.127 252 119 8 5 241 87 306 1.44e-28 114
Msa1204460 AT5G24010.1 36.078 255 118 10 5 241 82 309 8.54e-28 111
Msa1204460 AT5G61350.1 32.780 241 142 8 5 241 87 311 4.45e-27 109
Msa1204460 AT4G39110.1 30.242 248 151 5 1 241 102 334 7.55e-25 103
Msa1204460 AT2G21480.1 29.839 248 152 5 1 241 101 333 9.66e-25 102
Msa1204460 AT5G59700.1 31.687 243 138 8 3 239 74 294 1.84e-24 102
Msa1204460 AT5G54380.1 33.333 243 139 6 5 241 80 305 1.23e-23 99.8
Msa1204460 AT2G39360.1 30.364 247 137 9 3 239 71 292 1.62e-22 96.3
Msa1204460 AT3G46290.1 38.824 170 91 5 3 171 74 231 5.02e-22 95.1
Msa1204460 AT1G30570.1 28.185 259 150 7 3 241 80 322 1.75e-19 87.4
Msa1204460 AT5G39000.1 30.709 254 139 10 6 241 83 317 2.45e-19 87.0
Msa1204460 AT5G39030.1 30.153 262 141 11 1 241 74 314 7.22e-19 85.9
Msa1204460 AT5G39030.2 30.153 262 141 11 1 241 68 308 9.76e-19 85.5
Msa1204460 AT5G39020.1 30.870 230 125 9 6 221 80 289 5.55e-18 83.2
Msa1204460 AT3G04690.1 29.200 250 146 10 6 241 77 309 1.14e-15 76.3
Msa1204460 AT3G51550.1 30.531 226 129 9 1 214 83 292 3.88e-15 74.7

Find 38 sgRNAs with CRISPR-Local

Find 54 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CGATAAAGTATCAATATTTC+TGG 0.166588 8_1:+60241914 None:intergenic
TTGATACTTTATCGAGAAAA+TGG 0.216656 8_1:-60241905 Msa1204460:CDS
GTCGATACTTATCTAATTAT+AGG 0.233175 8_1:-60242001 Msa1204460:CDS
GCAGTTTGATAAATAATATC+TGG 0.290669 8_1:+60241759 None:intergenic
TCGATACTTATCTAATTATA+GGG 0.306393 8_1:-60242000 Msa1204460:CDS
CGTACCATGTAGGTGTTGTT+TGG 0.333074 8_1:+60242305 None:intergenic
AAATTCAACGTTTCTGTTCC+CGG 0.339246 8_1:-60242236 Msa1204460:CDS
GCAATATATTGATTTGAATC+TGG 0.357246 8_1:+60241783 None:intergenic
AATGGAAAATTCTTGCAGTT+TGG 0.378288 8_1:+60242357 None:intergenic
GTGAAGAGAATGAAAAGAAA+TGG 0.389396 8_1:+60242279 None:intergenic
CAGTTTCTCCTCCGACGTTA+AGG 0.429547 8_1:+60241940 None:intergenic
TTTGCAGTGGAAAGGTTAGT+TGG 0.435305 8_1:+60242257 None:intergenic
AGTAAACTGGTACGAAGATT+CGG 0.439498 8_1:+60242334 None:intergenic
ATTGAATCGCCCAATTGAAT+CGG 0.443574 8_1:+60242040 None:intergenic
GAATCGGGGATTAAAAGAAC+AGG 0.444089 8_1:+60242056 None:intergenic
GTACCATGTAGGTGTTGTTT+GGG 0.451814 8_1:+60242306 None:intergenic
CTAACGATTTAAGCATAAGT+TGG 0.452424 8_1:-60241716 Msa1204460:CDS
TTGAATCGCCCAATTGAATC+GGG 0.457093 8_1:+60242041 None:intergenic
TTCAATTACAACGATTCTAC+TGG 0.479886 8_1:-60242023 Msa1204460:CDS
GCAGTTTGGTAGAGAGATGA+AGG 0.490787 8_1:+60242371 None:intergenic
TGTTTGGGAAGGTAGTAAAC+TGG 0.492724 8_1:+60242321 None:intergenic
TTAGTTATATAAATGTCATC+TGG 0.498378 8_1:+60241879 None:intergenic
CTTCCCAAACAACACCTACA+TGG 0.519905 8_1:-60242309 Msa1204460:CDS
TTGATTTGAATCTGGACCAT+CGG 0.556569 8_1:+60241791 None:intergenic
CATGTAGGTGTTGTTTGGGA+AGG 0.568609 8_1:+60242310 None:intergenic
TACTTATCTAATTATAGGGG+CGG 0.573305 8_1:-60241996 Msa1204460:CDS
TGATCTATATTCTTCTCCAC+AGG 0.573367 8_1:+60241687 None:intergenic
ACTGGTACGAAGATTCGGAA+TGG 0.590962 8_1:+60242339 None:intergenic
CATAAGTTGGAGTGTTCCTG+TGG 0.602870 8_1:-60241703 Msa1204460:CDS
CGATACTTATCTAATTATAG+GGG 0.612644 8_1:-60241999 Msa1204460:CDS
GAAATGGAAACGTACCATGT+AGG 0.613092 8_1:+60242295 None:intergenic
TATAGCATTAACAAACGCGA+AGG 0.635159 8_1:+60242094 None:intergenic
TTTCTCCTCCGACGTTAAGG+CGG 0.638143 8_1:+60241943 None:intergenic
ACAAAACACCGCCTTAACGT+CGG 0.655567 8_1:-60241951 Msa1204460:CDS
TGAATCGCCCAATTGAATCG+GGG 0.666832 8_1:+60242042 None:intergenic
AAACACCGCCTTAACGTCGG+AGG 0.677354 8_1:-60241948 Msa1204460:CDS
ACTGCAGATGATGAGTCCGA+TGG 0.684779 8_1:-60241807 Msa1204460:CDS
AATCGGGGATTAAAAGAACA+GGG 0.712103 8_1:+60242057 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TCGATACTTATCTAATTATA+GGG - chr8_1:60242045-60242064 Msa1204460:CDS 20.0%
!! TTAGTTATATAAATGTCATC+TGG + chr8_1:60242169-60242188 None:intergenic 20.0%
!!! GCTCAAAATAGTTTATTTTT+TGG - chr8_1:60242199-60242218 Msa1204460:CDS 20.0%
!!! CAAAATAGTTTATTTTTTGG+AGG - chr8_1:60242202-60242221 Msa1204460:CDS 20.0%
! GTCGATACTTATCTAATTAT+AGG - chr8_1:60242044-60242063 Msa1204460:CDS 25.0%
! CGATACTTATCTAATTATAG+GGG - chr8_1:60242046-60242065 Msa1204460:CDS 25.0%
!! CGATAAAGTATCAATATTTC+TGG + chr8_1:60242134-60242153 None:intergenic 25.0%
! TTGATACTTTATCGAGAAAA+TGG - chr8_1:60242140-60242159 Msa1204460:CDS 25.0%
!!! GCAATATATTGATTTGAATC+TGG + chr8_1:60242265-60242284 None:intergenic 25.0%
! GCAGTTTGATAAATAATATC+TGG + chr8_1:60242289-60242308 None:intergenic 25.0%
AATGGAAAATTCTTGCAGTT+TGG + chr8_1:60241691-60241710 None:intergenic 30.0%
GTGAAGAGAATGAAAAGAAA+TGG + chr8_1:60241769-60241788 None:intergenic 30.0%
! ATTTTGTAACAGAGAGAAAC+CGG + chr8_1:60241831-60241850 None:intergenic 30.0%
! ACGTAGTACTCTTTTACTAA+AGG + chr8_1:60241881-60241900 None:intergenic 30.0%
! TGTGAAAGTGATTTTGAATC+TGG + chr8_1:60241918-60241937 None:intergenic 30.0%
! TTTTAATCCCCGATTCAATT+GGG - chr8_1:60241996-60242015 Msa1204460:CDS 30.0%
TTCAATTACAACGATTCTAC+TGG - chr8_1:60242022-60242041 Msa1204460:CDS 30.0%
TACTTATCTAATTATAGGGG+CGG - chr8_1:60242049-60242068 Msa1204460:CDS 30.0%
!! AAACTATTTTGAGCGTTAAG+TGG + chr8_1:60242193-60242212 None:intergenic 30.0%
ACTGCTAAAGAGAGTAAAAA+CGG - chr8_1:60242304-60242323 Msa1204460:CDS 30.0%
CTAACGATTTAAGCATAAGT+TGG - chr8_1:60242329-60242348 Msa1204460:CDS 30.0%
AGTAAACTGGTACGAAGATT+CGG + chr8_1:60241714-60241733 None:intergenic 35.0%
! AGAAACGTTGAATTTTGCAG+TGG + chr8_1:60241804-60241823 None:intergenic 35.0%
AAATTCAACGTTTCTGTTCC+CGG - chr8_1:60241809-60241828 Msa1204460:CDS 35.0%
! TTTTGTAACAGAGAGAAACC+GGG + chr8_1:60241830-60241849 None:intergenic 35.0%
! TTTTACTAAAGGAGACTTGG+TGG + chr8_1:60241870-60241889 None:intergenic 35.0%
! CTCTTTTACTAAAGGAGACT+TGG + chr8_1:60241873-60241892 None:intergenic 35.0%
TATAGCATTAACAAACGCGA+AGG + chr8_1:60241954-60241973 None:intergenic 35.0%
AATCGGGGATTAAAAGAACA+GGG + chr8_1:60241991-60242010 None:intergenic 35.0%
! CTTTTAATCCCCGATTCAAT+TGG - chr8_1:60241995-60242014 Msa1204460:CDS 35.0%
ATTGAATCGCCCAATTGAAT+CGG + chr8_1:60242008-60242027 None:intergenic 35.0%
! TTGATTTGAATCTGGACCAT+CGG + chr8_1:60242257-60242276 None:intergenic 35.0%
TGATCTATATTCTTCTCCAC+AGG + chr8_1:60242361-60242380 None:intergenic 35.0%
TGTTTGGGAAGGTAGTAAAC+TGG + chr8_1:60241727-60241746 None:intergenic 40.0%
!! GTACCATGTAGGTGTTGTTT+GGG + chr8_1:60241742-60241761 None:intergenic 40.0%
GAAATGGAAACGTACCATGT+AGG + chr8_1:60241753-60241772 None:intergenic 40.0%
TTTGCAGTGGAAAGGTTAGT+TGG + chr8_1:60241791-60241810 None:intergenic 40.0%
! CGTTGAATTTTGCAGTGGAA+AGG + chr8_1:60241799-60241818 None:intergenic 40.0%
! AACGCGAAGGATAAGTTTTG+AGG + chr8_1:60241941-60241960 None:intergenic 40.0%
GAATCGGGGATTAAAAGAAC+AGG + chr8_1:60241992-60242011 None:intergenic 40.0%
TTGAATCGCCCAATTGAATC+GGG + chr8_1:60242007-60242026 None:intergenic 40.0%
GCAGTTTGGTAGAGAGATGA+AGG + chr8_1:60241677-60241696 None:intergenic 45.0%
ACTGGTACGAAGATTCGGAA+TGG + chr8_1:60241709-60241728 None:intergenic 45.0%
!! CATGTAGGTGTTGTTTGGGA+AGG + chr8_1:60241738-60241757 None:intergenic 45.0%
CTTCCCAAACAACACCTACA+TGG - chr8_1:60241736-60241755 Msa1204460:CDS 45.0%
!! CGTACCATGTAGGTGTTGTT+TGG + chr8_1:60241743-60241762 None:intergenic 45.0%
TGAATCGCCCAATTGAATCG+GGG + chr8_1:60242006-60242025 None:intergenic 45.0%
ACAAAACACCGCCTTAACGT+CGG - chr8_1:60242094-60242113 Msa1204460:CDS 45.0%
! CATAAGTTGGAGTGTTCCTG+TGG - chr8_1:60242342-60242361 Msa1204460:CDS 45.0%
TTTCTCCTCCGACGTTAAGG+CGG + chr8_1:60242105-60242124 None:intergenic 50.0%
CAGTTTCTCCTCCGACGTTA+AGG + chr8_1:60242108-60242127 None:intergenic 50.0%
ACTGCAGATGATGAGTCCGA+TGG - chr8_1:60242238-60242257 Msa1204460:CDS 50.0%
CGGTTTACACTCTCGAGCGT+TGG - chr8_1:60242069-60242088 Msa1204460:CDS 55.0%
AAACACCGCCTTAACGTCGG+AGG - chr8_1:60242097-60242116 Msa1204460:CDS 55.0%
Chromosome Type Strat End Strand Name
chr8_1 gene 60241671 60242396 60241671 ID=Msa1204460;Name=Msa1204460
chr8_1 mRNA 60241671 60242396 60241671 ID=Msa1204460-mRNA-1;Parent=Msa1204460;Name=Msa1204460-mRNA-1;_AED=0.44;_eAED=0.44;_QI=0|-1|0|1|-1|1|1|0|241
chr8_1 exon 60241671 60242396 60241671 ID=Msa1204460-mRNA-1:exon:19524;Parent=Msa1204460-mRNA-1
chr8_1 CDS 60241671 60242396 60241671 ID=Msa1204460-mRNA-1:cds;Parent=Msa1204460-mRNA-1
Gene Sequence

>Msa1204460

ATGCCTTCATCTCTCTACCAAACTGCAAGAATTTTCCATTCCGAATCTTCGTACCAGTTTACTACCTTCCCAAACAACACCTACATGGTACGTTTCCATTTCTTTTCATTCTCTTCACCAACTAACCTTTCCACTGCAAAATTCAACGTTTCTGTTCCCGGTTTCTCTCTGTTACAAAATTTTGATGCAAAAAACACCACCAAGTCTCCTTTAGTAAAAGAGTACTACGTTAAAATCAACATAACCAGATTCAAAATCACTTTCACACCTCAAAACTTATCCTTCGCGTTTGTTAATGCTATAGAACTCTTTCTGCTCCCTGTTCTTTTAATCCCCGATTCAATTGGGCGATTCAATTACAACGATTCTACTGGTCGATACTTATCTAATTATAGGGGCGGTTTACACTCTCGAGCGTTGGAAACAAAACACCGCCTTAACGTCGGAGGAGAAACTGTCACCAGAAATATTGATACTTTATCGAGAAAATGGTTACCAGATGACATTTATATAACTAATCCACTTAACGCTCAAAATAGTTTATTTTTTGGAGGTACAATTAAACGCACTGCAGATGATGAGTCCGATGGTCCAGATTCAAATCAATATATTGCTCCAGATATTATTTATCAAACTGCTAAAGAGAGTAAAAACGGTTCTAACGATTTAAGCATAAGTTGGAGTGTTCCTGTGGAGAAGAATATAGATCATTTCCTTAATTTATGA
Protein sequence

>Msa1204460

MPSSLYQTARIFHSESSYQFTTFPNNTYMVRFHFFSFSSPTNLSTAKFNVSVPGFSLLQNFDAKNTTKSPLVKEYYVKINITRFKITFTPQNLSFAFVNAIELFLLPVLLIPDSIGRFNYNDSTGRYLSNYRGGLHSRALETKHRLNVGGETVTRNIDTLSRKWLPDDIYITNPLNAQNSLFFGGTIKRTADDESDGPDSNQYIAPDIIYQTAKESKNGSNDLSISWSVPVEKNIDHFLNL*