AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1391050

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1391050 MtrunA17_Chr1g0182181 95.122 164 8 0 5 168 2 165 3.62e-114 320
Msa1391050 MtrunA17_Chr7g0263121 64.327 171 53 4 1 165 1 169 5.51e-71 211
Msa1391050 MtrunA17_Chr1g0182161 63.429 175 47 8 1 166 2 168 8.18e-63 191
Msa1391050 MtrunA17_Chr7g0263131 58.896 163 57 5 1 162 3 156 9.55e-58 178
Msa1391050 MtrunA17_Chr2g0327901 49.677 155 49 6 1 153 1 128 1.10e-35 120
Msa1391050 MtrunA17_Chr1g0212561 41.262 206 77 8 1 167 1 201 2.00e-33 117
Msa1391050 MtrunA17_Chr7g0222831 52.101 119 49 3 1 115 1 115 4.67e-32 113
Msa1391050 MtrunA17_Chr2g0320311 32.314 229 61 7 7 154 68 283 3.09e-22 90.5
Msa1391050 MtrunA17_Chr1g0197281 34.826 201 65 7 10 146 98 296 2.46e-21 89.0
Msa1391050 MtrunA17_Chr1g0180311 38.095 147 45 3 13 113 80 226 1.84e-19 82.8
Msa1391050 MtrunA17_Chr1g0207451 41.584 101 54 2 14 112 60 157 3.19e-17 76.3
Msa1391050 MtrunA17_Chr4g0012691 46.429 84 35 2 38 111 220 303 4.55e-16 74.3
Msa1391050 MtrunA17_Chr4g0027991 31.707 164 56 3 38 154 113 267 6.44e-16 73.2
Msa1391050 MtrunA17_Chr7g0231181 38.983 118 54 6 38 152 240 342 1.87e-15 72.4
Msa1391050 MtrunA17_Chr3g0134711 36.620 142 66 5 2 119 37 178 6.99e-14 67.0
Msa1391050 MtrunA17_Chr1g0152661 36.066 122 58 4 36 146 79 191 2.72e-13 65.5
Msa1391050 MtrunA17_Chr1g0188911 34.783 115 34 3 38 112 44 157 7.98e-13 63.5
Msa1391050 MtrunA17_Chr1g0188901 40.000 95 42 3 38 117 60 154 1.10e-12 62.8
Msa1391050 MtrunA17_Chr4g0061301 33.333 126 45 3 38 124 348 473 7.75e-12 62.4
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1391050 AT2G37430.1 45.251 179 84 6 1 168 1 176 1.10e-42 140
Msa1391050 AT3G53600.1 43.956 182 79 7 1 168 1 173 1.04e-36 125
Msa1391050 AT2G28710.1 46.061 165 69 7 1 158 1 152 9.93e-33 114
Msa1391050 AT5G59820.1 45.455 154 71 5 11 158 12 158 5.73e-29 105
Msa1391050 AT2G28200.1 35.714 196 73 7 10 154 73 266 2.16e-26 101
Msa1391050 AT3G46090.1 43.293 164 67 6 9 158 11 162 2.45e-26 98.6
Msa1391050 AT3G46080.1 43.902 164 75 7 5 158 4 160 7.61e-26 97.1
Msa1391050 AT3G46070.1 40.491 163 79 7 1 151 1 157 1.75e-22 88.6
Msa1391050 AT5G03510.1 41.497 147 39 6 10 109 69 215 1.02e-21 89.4
Msa1391050 AT5G04390.1 36.471 170 47 5 1 112 89 255 1.31e-20 87.4
Msa1391050 AT3G10470.1 44.660 103 26 2 38 109 182 284 1.91e-18 81.6
Msa1391050 AT2G45120.1 36.196 163 74 5 13 152 150 305 1.02e-17 79.0
Msa1391050 AT3G60580.1 32.530 166 76 4 13 152 126 281 1.49e-16 75.5
Msa1391050 AT1G02030.1 48.718 78 39 1 38 114 160 237 1.04e-15 72.8
Msa1391050 AT1G27730.1 33.113 151 87 4 9 149 50 196 3.03e-15 70.9
Msa1391050 AT1G49900.1 36.667 120 70 3 25 140 735 852 9.17e-15 71.6
Msa1391050 AT1G49900.1 33.582 134 85 2 38 167 193 326 3.32e-13 67.0
Msa1391050 AT3G49930.1 37.931 116 47 5 14 108 60 171 4.25e-14 67.8
Msa1391050 AT5G43170.1 34.247 146 77 5 9 151 45 174 3.66e-13 64.7
Msa1391050 AT5G56200.1 44.444 90 29 2 40 108 344 433 6.68e-13 65.9
Msa1391050 AT4G35280.1 39.286 112 50 3 10 108 138 244 7.62e-13 65.1
Msa1391050 AT3G19580.1 34.646 127 61 5 4 108 61 187 1.38e-12 64.3
Msa1391050 AT3G19580.2 34.646 127 61 5 4 108 61 187 1.38e-12 64.3
Msa1391050 AT5G67450.1 37.363 91 38 2 37 108 96 186 1.68e-12 63.9
Msa1391050 AT5G04340.1 41.176 85 39 2 38 111 89 173 1.74e-11 60.8

Find 41 sgRNAs with CRISPR-Local

Find 50 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTTCTTTGGTTTGGTTTCTT+TGG 0.133578 tig0021402:+103431 None:intergenic
TTCTCTCTTGGCCAGGCTTT+GGG 0.201073 tig0021402:-103219 Msa1391050:CDS
GAAGTTATTGTTCGGAAATA+TGG 0.242022 tig0021402:-103043 Msa1391050:CDS
AAGCTACATGCCCAAACTTT+AGG 0.279584 tig0021402:-103291 Msa1391050:CDS
TTCTTTGGTTTGGTTTCTTT+GGG 0.287528 tig0021402:+103432 None:intergenic
ACAGGACTAAAATGTTTCTT+TGG 0.294036 tig0021402:+103417 None:intergenic
TATTCAGCAAACCTAAAGTT+TGG 0.298957 tig0021402:+103280 None:intergenic
ACTAAAATGTTTCTTTGGTT+TGG 0.313841 tig0021402:+103422 None:intergenic
GAGTTTCACGGTATCTAGTT+TGG 0.314780 tig0021402:+103314 None:intergenic
ATTCTCTCTTGGCCAGGCTT+TGG 0.331279 tig0021402:-103220 Msa1391050:CDS
TGAAAAGATCGAATAGTAAG+AGG 0.344770 tig0021402:-103110 Msa1391050:CDS
AGTTTCACGGTATCTAGTTT+GGG 0.350342 tig0021402:+103315 None:intergenic
AATGTAGCACCCATGCGTTT+TGG 0.353287 tig0021402:+103254 None:intergenic
ATTCAGCAAACCTAAAGTTT+GGG 0.384341 tig0021402:+103281 None:intergenic
AAGAGTGGAGAATATAGATT+TGG 0.395790 tig0021402:-103481 Msa1391050:CDS
CATATGAGAAGGCACAAAAT+TGG 0.403275 tig0021402:-103192 Msa1391050:CDS
AATGACTTGAAGTTATTGTT+CGG 0.424062 tig0021402:-103051 Msa1391050:CDS
TGTGGTAAAGAATTCTCTCT+TGG 0.452482 tig0021402:-103231 Msa1391050:CDS
CTGAATAACCCCAAAACGCA+TGG 0.471935 tig0021402:-103264 Msa1391050:CDS
TTAATTTCGTAGCCATGAAA+AGG 0.477789 tig0021402:-103515 None:intergenic
ACGCATGGGTGCTACATTTG+TGG 0.490183 tig0021402:-103249 Msa1391050:CDS
GGCATGTAGCTTGAGTTTCA+CGG 0.491665 tig0021402:+103302 None:intergenic
TCATATGTCCTCCCAAAGCC+TGG 0.497850 tig0021402:+103208 None:intergenic
TAGTAAGAGGGTTATGTGCT+TGG 0.501643 tig0021402:-103097 Msa1391050:CDS
TAAAGAATTCTCTCTTGGCC+AGG 0.519657 tig0021402:-103226 Msa1391050:CDS
TTCTCTTCGTTTCAAGCCCT+AGG 0.530440 tig0021402:-103363 Msa1391050:CDS
GAAAAGATCGAATAGTAAGA+GGG 0.539509 tig0021402:-103109 Msa1391050:CDS
TCTCTTGGCCAGGCTTTGGG+AGG 0.541746 tig0021402:-103216 Msa1391050:CDS
GACTAGCTCTATGGCCACCT+AGG 0.545631 tig0021402:+103346 None:intergenic
CACAAAATTGGCGTCAACGA+GGG 0.547186 tig0021402:-103180 Msa1391050:CDS
TTTCTTTGGGATGAGAGAGT+AGG 0.548800 tig0021402:+103445 None:intergenic
AAGGCAGAGAGACGAAAGAG+TGG 0.561042 tig0021402:-103496 Msa1391050:CDS
ACTAGCTCTATGGCCACCTA+GGG 0.585030 tig0021402:+103347 None:intergenic
AACTTCAAGTCATTCTGCAA+AGG 0.606866 tig0021402:+103060 None:intergenic
TGAATAACCCCAAAACGCAT+GGG 0.610752 tig0021402:-103263 Msa1391050:CDS
GTGGTGCACTCAAATTCCAC+AGG 0.615607 tig0021402:+103399 None:intergenic
CTTTGGGAGGACATATGAGA+AGG 0.632803 tig0021402:-103203 Msa1391050:CDS
TCTTCGTTTCAAGCCCTAGG+TGG 0.635082 tig0021402:-103360 Msa1391050:CDS
CTTGAAACGAAGAGAACTTG+CGG 0.655759 tig0021402:+103370 None:intergenic
AGAGAACTTGCGGTTGCATG+TGG 0.663988 tig0021402:+103380 None:intergenic
GCACAAAATTGGCGTCAACG+AGG 0.669929 tig0021402:-103181 Msa1391050:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TATTCGATCTTTTCAATATT+GGG + tig0021402:103403-103422 None:intergenic 20.0%
! ACTAAAATGTTTCTTTGGTT+TGG + tig0021402:103099-103118 None:intergenic 25.0%
! TTCTTTGGTGAAGAAAAATA+AGG - tig0021402:103364-103383 Msa1391050:CDS 25.0%
!! CTATTCGATCTTTTCAATAT+TGG + tig0021402:103404-103423 None:intergenic 25.0%
! AATGACTTGAAGTTATTGTT+CGG - tig0021402:103467-103486 Msa1391050:CDS 25.0%
! CAAAAAAATGAATCAACTTC+AGG + tig0021402:103503-103522 None:intergenic 25.0%
AAGAGTGGAGAATATAGATT+TGG - tig0021402:103037-103056 Msa1391050:CDS 30.0%
!! TTCTTTGGTTTGGTTTCTTT+GGG + tig0021402:103089-103108 None:intergenic 30.0%
!! TTTCTTTGGTTTGGTTTCTT+TGG + tig0021402:103090-103109 None:intergenic 30.0%
ACAGGACTAAAATGTTTCTT+TGG + tig0021402:103104-103123 None:intergenic 30.0%
!! AAAGAAACATTTTAGTCCTG+TGG - tig0021402:103103-103122 Msa1391050:CDS 30.0%
ATTCAGCAAACCTAAAGTTT+GGG + tig0021402:103240-103259 None:intergenic 30.0%
TATTCAGCAAACCTAAAGTT+TGG + tig0021402:103241-103260 None:intergenic 30.0%
GTGAAGAAAAATAAGGTTGT+TGG - tig0021402:103371-103390 Msa1391050:CDS 30.0%
TGAAAAGATCGAATAGTAAG+AGG - tig0021402:103408-103427 Msa1391050:CDS 30.0%
GAAAAGATCGAATAGTAAGA+GGG - tig0021402:103409-103428 Msa1391050:CDS 30.0%
GAAGTTATTGTTCGGAAATA+TGG - tig0021402:103475-103494 Msa1391050:CDS 30.0%
! AGTTTCACGGTATCTAGTTT+GGG + tig0021402:103206-103225 None:intergenic 35.0%
TGTGGTAAAGAATTCTCTCT+TGG - tig0021402:103287-103306 Msa1391050:CDS 35.0%
! CATATGAGAAGGCACAAAAT+TGG - tig0021402:103326-103345 Msa1391050:CDS 35.0%
AACTTCAAGTCATTCTGCAA+AGG + tig0021402:103461-103480 None:intergenic 35.0%
!! TTTCTTTGGGATGAGAGAGT+AGG + tig0021402:103076-103095 None:intergenic 40.0%
CTTGAAACGAAGAGAACTTG+CGG + tig0021402:103151-103170 None:intergenic 40.0%
!!! GCTTTTTGTGACTAGCTCTA+TGG + tig0021402:103184-103203 None:intergenic 40.0%
GAGTTTCACGGTATCTAGTT+TGG + tig0021402:103207-103226 None:intergenic 40.0%
AAGCTACATGCCCAAACTTT+AGG - tig0021402:103227-103246 Msa1391050:CDS 40.0%
TGAATAACCCCAAAACGCAT+GGG - tig0021402:103255-103274 Msa1391050:CDS 40.0%
TAAAGAATTCTCTCTTGGCC+AGG - tig0021402:103292-103311 Msa1391050:CDS 40.0%
TAGTAAGAGGGTTATGTGCT+TGG - tig0021402:103421-103440 Msa1391050:CDS 40.0%
TTCTCTTCGTTTCAAGCCCT+AGG - tig0021402:103155-103174 Msa1391050:CDS 45.0%
GGCATGTAGCTTGAGTTTCA+CGG + tig0021402:103219-103238 None:intergenic 45.0%
CTGAATAACCCCAAAACGCA+TGG - tig0021402:103254-103273 Msa1391050:CDS 45.0%
! ATGTAGCACCCATGCGTTTT+GGG + tig0021402:103266-103285 None:intergenic 45.0%
! AATGTAGCACCCATGCGTTT+TGG + tig0021402:103267-103286 None:intergenic 45.0%
! CTTTGGGAGGACATATGAGA+AGG - tig0021402:103315-103334 Msa1391050:CDS 45.0%
CACAAAATTGGCGTCAACGA+GGG - tig0021402:103338-103357 Msa1391050:CDS 45.0%
! CGTCAACGAGGGATTTTCTT+TGG - tig0021402:103349-103368 Msa1391050:CDS 45.0%
AAGGCAGAGAGACGAAAGAG+TGG - tig0021402:103022-103041 Msa1391050:CDS 50.0%
GTGGTGCACTCAAATTCCAC+AGG + tig0021402:103122-103141 None:intergenic 50.0%
AGAGAACTTGCGGTTGCATG+TGG + tig0021402:103141-103160 None:intergenic 50.0%
TCTTCGTTTCAAGCCCTAGG+TGG - tig0021402:103158-103177 Msa1391050:CDS 50.0%
!! ACTAGCTCTATGGCCACCTA+GGG + tig0021402:103174-103193 None:intergenic 50.0%
! TGTAGCACCCATGCGTTTTG+GGG + tig0021402:103265-103284 None:intergenic 50.0%
! ACGCATGGGTGCTACATTTG+TGG - tig0021402:103269-103288 Msa1391050:CDS 50.0%
ATTCTCTCTTGGCCAGGCTT+TGG - tig0021402:103298-103317 Msa1391050:CDS 50.0%
TTCTCTCTTGGCCAGGCTTT+GGG - tig0021402:103299-103318 Msa1391050:CDS 50.0%
TCATATGTCCTCCCAAAGCC+TGG + tig0021402:103313-103332 None:intergenic 50.0%
GCACAAAATTGGCGTCAACG+AGG - tig0021402:103337-103356 Msa1391050:CDS 50.0%
!! GACTAGCTCTATGGCCACCT+AGG + tig0021402:103175-103194 None:intergenic 55.0%
!! TCTCTTGGCCAGGCTTTGGG+AGG - tig0021402:103302-103321 Msa1391050:CDS 60.0%
Chromosome Type Strat End Strand Name
tig0021402 gene 103017 103523 103017 ID=Msa1391050;Name=Msa1391050
tig0021402 mRNA 103017 103523 103017 ID=Msa1391050-mRNA-1;Parent=Msa1391050;Name=Msa1391050-mRNA-1;_AED=0.01;_eAED=0.01;_QI=0|-1|0|1|-1|1|1|0|168
tig0021402 exon 103017 103523 103017 ID=Msa1391050-mRNA-1:exon:12519;Parent=Msa1391050-mRNA-1
tig0021402 CDS 103017 103523 103017 ID=Msa1391050-mRNA-1:cds;Parent=Msa1391050-mRNA-1
Gene Sequence

>Msa1391050

ATGAAAAGGCAGAGAGACGAAAGAGTGGAGAATATAGATTTGGCAAATTGTCTAATCCTACTCTCTCATCCCAAAGAAACCAAACCAAAGAAACATTTTAGTCCTGTGGAATTTGAGTGCACCACATGCAACCGCAAGTTCTCTTCGTTTCAAGCCCTAGGTGGCCATAGAGCTAGTCACAAAAAGCCCAAACTAGATACCGTGAAACTCAAGCTACATGCCCAAACTTTAGGTTTGCTGAATAACCCCAAAACGCATGGGTGCTACATTTGTGGTAAAGAATTCTCTCTTGGCCAGGCTTTGGGAGGACATATGAGAAGGCACAAAATTGGCGTCAACGAGGGATTTTCTTTGGTGAAGAAAAATAAGGTTGTTGGAAAAATCCCAATATTGAAAAGATCGAATAGTAAGAGGGTTATGTGCTTGGACTTGAACTTAACACCTTTGCAGAATGACTTGAAGTTATTGTTCGGAAATATGGCACCTGAAGTTGATTCATTTTTTTGA
Protein sequence

>Msa1391050

MKRQRDERVENIDLANCLILLSHPKETKPKKHFSPVEFECTTCNRKFSSFQALGGHRASHKKPKLDTVKLKLHAQTLGLLNNPKTHGCYICGKEFSLGQALGGHMRRHKIGVNEGFSLVKKNKVVGKIPILKRSNSKRVMCLDLNLTPLQNDLKLLFGNMAPEVDSFF*