AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene068294

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene068294.t1 MTR_4g013345 87.755 196 24 0 1 196 1 196 2.58e-120 338
MS.gene068294.t1 MTR_4g013350 85.279 197 28 1 1 196 1 197 3.12e-118 333
MS.gene068294.t1 MTR_4g013330 78.894 199 39 2 1 196 1 199 8.47e-110 312
MS.gene068294.t1 MTR_4g013335 78.022 182 37 2 16 196 17 196 2.33e-105 301
MS.gene068294.t1 MTR_4g013320 75.000 184 43 2 16 196 16 199 1.54e-102 294
MS.gene068294.t1 MTR_4g013325 74.000 200 47 3 1 196 1 199 1.27e-90 264
MS.gene068294.t1 MTR_4g013310 66.332 199 62 2 1 196 1 197 8.25e-88 256
MS.gene068294.t1 MTR_7g070390 64.583 192 66 2 6 196 2 192 1.01e-81 241
MS.gene068294.t1 MTR_4g013385 58.511 188 73 3 9 196 8 190 1.50e-76 228
MS.gene068294.t1 MTR_0433s0040 58.511 188 73 3 9 196 8 190 1.50e-76 228
MS.gene068294.t1 MTR_1g054525 57.592 191 76 2 9 196 4 192 5.00e-71 214
MS.gene068294.t1 MTR_4g013770 58.333 168 67 2 30 196 26 191 1.61e-64 197
MS.gene068294.t1 MTR_4g013355 52.660 188 75 3 9 196 6 179 1.17e-62 192
MS.gene068294.t1 MTR_7g093850 49.189 185 92 2 13 196 11 194 3.52e-59 184
MS.gene068294.t1 MTR_7g093820 49.189 185 92 2 13 196 11 194 7.30e-59 183
MS.gene068294.t1 MTR_7g093830 47.027 185 96 2 13 196 10 193 2.03e-57 179
MS.gene068294.t1 MTR_4g073950 52.632 152 71 1 46 196 41 192 4.31e-56 176
MS.gene068294.t1 MTR_7g093870 50.581 172 79 3 30 196 23 193 1.02e-54 173
MS.gene068294.t1 MTR_7g093790 46.386 166 87 2 32 196 27 191 3.56e-54 171
MS.gene068294.t1 MTR_3g105640 47.205 161 83 2 38 196 28 188 5.57e-46 150
MS.gene068294.t1 MTR_1g056370 47.682 151 77 2 46 195 36 185 3.02e-45 148
MS.gene068294.t1 MTR_3g105630 41.709 199 103 4 1 196 1 189 4.37e-44 145
MS.gene068294.t1 MTR_4g078885 45.638 149 79 1 48 196 39 185 6.38e-44 145
MS.gene068294.t1 MTR_3g034030 46.309 149 78 1 48 196 39 185 1.33e-43 144
MS.gene068294.t1 MTR_5g096120 42.949 156 77 3 49 196 38 189 7.23e-40 134
MS.gene068294.t1 MTR_4g122110 36.170 141 90 0 56 196 40 180 6.71e-28 103
MS.gene068294.t1 MTR_4g122130 35.211 142 92 0 55 196 39 180 3.96e-25 96.7
MS.gene068294.t1 MTR_4g049570 28.671 143 102 0 49 191 31 173 1.36e-16 74.3
MS.gene068294.t1 MTR_4g049550 30.709 127 88 0 45 171 27 153 1.76e-16 73.9
MS.gene068294.t1 MTR_8g099115 33.824 136 81 3 48 175 34 168 3.73e-16 73.2
MS.gene068294.t1 MTR_8g099135 35.821 134 67 5 55 175 37 164 9.26e-15 69.7
MS.gene068294.t1 MTR_1g115510 32.787 122 71 4 83 195 234 353 5.96e-11 60.8
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene068294.t1 AT1G55210 61.702 188 68 2 9 196 4 187 1.17e-81 241
MS.gene068294.t1 AT1G55210 61.702 188 68 2 9 196 4 187 1.17e-81 241
MS.gene068294.t1 AT5G49040 55.851 188 83 0 9 196 4 191 3.73e-76 227
MS.gene068294.t1 AT1G58170 57.447 188 68 2 12 196 7 185 1.82e-75 225
MS.gene068294.t1 AT3G13650 53.476 187 83 2 10 196 4 186 4.09e-70 211
MS.gene068294.t1 AT5G49030 56.069 173 76 0 9 181 4 176 1.24e-60 204
MS.gene068294.t1 AT3G13662 57.432 148 60 1 35 182 27 171 6.23e-57 177
MS.gene068294.t1 AT1G65870 50.331 151 75 0 45 195 39 189 1.76e-54 172
MS.gene068294.t1 AT2G21100 41.026 195 107 1 1 195 1 187 3.56e-52 166
MS.gene068294.t1 AT2G21100 41.026 195 107 1 1 195 1 187 3.56e-52 166
MS.gene068294.t1 AT3G13660 65.254 118 41 0 79 196 8 125 7.43e-52 163
MS.gene068294.t1 AT1G22900 50.993 151 72 1 45 195 45 193 4.89e-51 163
MS.gene068294.t1 AT5G42500 50.667 150 72 1 46 195 38 185 1.34e-50 162
MS.gene068294.t1 AT5G42510 48.667 150 75 1 46 195 35 182 4.59e-49 158
MS.gene068294.t1 AT3G58090 51.818 110 53 0 86 195 162 271 1.19e-38 134
MS.gene068294.t1 AT4G38700 42.308 156 84 3 47 196 35 190 1.27e-38 131
MS.gene068294.t1 AT2G21110 38.065 155 92 1 46 196 32 186 3.69e-35 122
MS.gene068294.t1 AT4G11210 33.103 145 88 4 39 179 27 166 1.36e-14 68.9
MS.gene068294.t1 AT4G23690 33.088 136 84 3 44 175 34 166 7.11e-14 67.4
MS.gene068294.t1 AT1G64160 31.967 122 76 3 52 169 37 155 8.89e-12 61.6
MS.gene068294.t1 AT4G11180 31.169 154 97 5 47 195 34 183 1.72e-11 60.8
MS.gene068294.t1 AT4G11190 27.857 140 94 3 44 179 30 166 7.88e-11 58.9

Find 30 sgRNAs with CRISPR-Local

Find 43 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTCACTGAAGGAAAGTATAA+TGG 0.310992 4.4:+86694081 MS.gene068294:CDS
ATTGACAACCCTTTGACTTT+AGG 0.312948 4.4:+86693961 MS.gene068294:CDS
TAAGTCATTTCAAATTATAT+TGG 0.313865 4.4:+86693842 MS.gene068294:CDS
CAACAAGCTTGGAACTCAAC+TGG 0.322818 4.4:-86693987 None:intergenic
GAACAAAGTGAGAAAATGTT+TGG 0.361732 4.4:-86693701 None:intergenic
GGGAGTACTATTACTATCTT+GGG 0.365410 4.4:+86694102 MS.gene068294:CDS
TGGGAGTACTATTACTATCT+TGG 0.368563 4.4:+86694101 MS.gene068294:CDS
TCTGCATCACAGGAAGAAAT+AGG 0.369275 4.4:+86694033 MS.gene068294:CDS
ATGCCTGTTGTTGGTGGTAG+TGG 0.372337 4.4:+86694156 MS.gene068294:CDS
CAAATAGATCGCAAGTTGTT+AGG 0.379691 4.4:+86693799 MS.gene068294:CDS
TATTGGCATGACATAATTAG+TGG 0.408932 4.4:+86693859 MS.gene068294:CDS
GGAACAATTGCAACCGAAGT+TGG 0.428664 4.4:-86693889 None:intergenic
CAGTTGAGTTCCAAGCTTGT+TGG 0.431032 4.4:+86693988 MS.gene068294:CDS
TCACTGAAGGAAAGTATAAT+GGG 0.445119 4.4:+86694082 MS.gene068294:CDS
GTTTGTTGCAAGAGATGAGA+AGG 0.446684 4.4:-86693729 None:intergenic
AACAAGCTTGGAACTCAACT+GGG 0.446836 4.4:-86693986 None:intergenic
TCCCTAACCTTATTAAAAGC+AGG 0.454908 4.4:-86694132 None:intergenic
ATGCTCAAGCTAGTACTCAT+TGG 0.460522 4.4:+86694202 MS.gene068294:CDS
TTTCTATGCATCTGCATCAC+AGG 0.485104 4.4:+86694023 MS.gene068294:CDS
AGTCCACTACCACCAACAAC+AGG 0.512977 4.4:-86694159 None:intergenic
AGGGAAATGCCTGTTGTTGG+TGG 0.521357 4.4:+86694150 MS.gene068294:CDS
TTGGATTGATGTCAAAGCTC+GGG 0.528314 4.4:+86694221 MS.gene068294:CDS
GTTAGGGAAATGCCTGTTGT+TGG 0.531572 4.4:+86694147 MS.gene068294:CDS
AAGCTTGTTGGAAAAGCTCA+AGG 0.537211 4.4:+86694000 MS.gene068294:CDS
ATTGGATTGATGTCAAAGCT+CGG 0.560589 4.4:+86694220 MS.gene068294:CDS
GTTGTTAGGCCTAAACAAGA+AGG 0.591926 4.4:+86693813 MS.gene068294:CDS
ACAAGCTTGGAACTCAACTG+GGG 0.651947 4.4:-86693985 None:intergenic
GTACTATTACTATCTTGGGG+AGG 0.673978 4.4:+86694106 MS.gene068294:CDS
CAAGCTTGGAACTCAACTGG+GGG 0.683629 4.4:-86693984 None:intergenic
GGAGTACTATTACTATCTTG+GGG 0.700411 4.4:+86694103 MS.gene068294:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TAAGTCATTTCAAATTATAT+TGG + chr4.4:86693842-86693861 MS.gene068294:CDS 15.0%
!!! GTAAACTCAACTACTTTTTT+TGG + chr4.4:86693925-86693944 MS.gene068294:CDS 25.0%
GAACAAAGTGAGAAAATGTT+TGG - chr4.4:86693704-86693723 None:intergenic 30.0%
TAGTGGAAAAAATCCAACTT+CGG + chr4.4:86693876-86693895 MS.gene068294:CDS 30.0%
TATTGGCATGACATAATTAG+TGG + chr4.4:86693859-86693878 MS.gene068294:CDS 30.0%
! ATGAATTTTGCTTTCACTGA+AGG + chr4.4:86694069-86694088 MS.gene068294:CDS 30.0%
! TCACTGAAGGAAAGTATAAT+GGG + chr4.4:86694082-86694101 MS.gene068294:CDS 30.0%
! TTCACTGAAGGAAAGTATAA+TGG + chr4.4:86694081-86694100 MS.gene068294:CDS 30.0%
!! ATCCTGCTTTTAATAAGGTT+AGG + chr4.4:86694130-86694149 MS.gene068294:CDS 30.0%
!! GTTGAGTTTACTTTTGATGA+TGG - chr4.4:86693916-86693935 None:intergenic 30.0%
!! TCCTGCTTTTAATAAGGTTA+GGG + chr4.4:86694131-86694150 MS.gene068294:CDS 30.0%
!! TTAGCTTTTCCTTCTTGTTT+AGG - chr4.4:86693825-86693844 None:intergenic 30.0%
ATTGGATTGATGTCAAAGCT+CGG + chr4.4:86694220-86694239 MS.gene068294:CDS 35.0%
CAAATAGATCGCAAGTTGTT+AGG + chr4.4:86693799-86693818 MS.gene068294:CDS 35.0%
TCCCTAACCTTATTAAAAGC+AGG - chr4.4:86694135-86694154 None:intergenic 35.0%
! ATTGACAACCCTTTGACTTT+AGG + chr4.4:86693961-86693980 MS.gene068294:CDS 35.0%
! GGAGTACTATTACTATCTTG+GGG + chr4.4:86694103-86694122 MS.gene068294:CDS 35.0%
!! GAGGAATCCTGCTTTTAATA+AGG + chr4.4:86694125-86694144 MS.gene068294:CDS 35.0%
!! GGGAGTACTATTACTATCTT+GGG + chr4.4:86694102-86694121 MS.gene068294:CDS 35.0%
!! TGGGAGTACTATTACTATCT+TGG + chr4.4:86694101-86694120 MS.gene068294:CDS 35.0%
!!! GAGTTTACTTTTGATGATGG+TGG - chr4.4:86693913-86693932 None:intergenic 35.0%
!!! GGACTTTTTAGATTTGCTAG+AGG + chr4.4:86694177-86694196 MS.gene068294:CDS 35.0%
AACAAGCTTGGAACTCAACT+GGG - chr4.4:86693989-86694008 None:intergenic 40.0%
ATGCTCAAGCTAGTACTCAT+TGG + chr4.4:86694202-86694221 MS.gene068294:CDS 40.0%
GTACTATTACTATCTTGGGG+AGG + chr4.4:86694106-86694125 MS.gene068294:CDS 40.0%
GTTGTTAGGCCTAAACAAGA+AGG + chr4.4:86693813-86693832 MS.gene068294:CDS 40.0%
TCTGCATCACAGGAAGAAAT+AGG + chr4.4:86694033-86694052 MS.gene068294:CDS 40.0%
TTGGATTGATGTCAAAGCTC+GGG + chr4.4:86694221-86694240 MS.gene068294:CDS 40.0%
TTTCTATGCATCTGCATCAC+AGG + chr4.4:86694023-86694042 MS.gene068294:CDS 40.0%
! GTTTGTTGCAAGAGATGAGA+AGG - chr4.4:86693732-86693751 None:intergenic 40.0%
! TTGAGCTTTTCCAACAAGCT+TGG - chr4.4:86694001-86694020 None:intergenic 40.0%
!! AAGCTTGTTGGAAAAGCTCA+AGG + chr4.4:86694000-86694019 MS.gene068294:CDS 40.0%
ACAAGCTTGGAACTCAACTG+GGG - chr4.4:86693988-86694007 None:intergenic 45.0%
CAACAAGCTTGGAACTCAAC+TGG - chr4.4:86693990-86694009 None:intergenic 45.0%
CAGTTGAGTTCCAAGCTTGT+TGG + chr4.4:86693988-86694007 MS.gene068294:CDS 45.0%
GGAACAATTGCAACCGAAGT+TGG - chr4.4:86693892-86693911 None:intergenic 45.0%
GTTAGGGAAATGCCTGTTGT+TGG + chr4.4:86694147-86694166 MS.gene068294:CDS 45.0%
AACTGGGGGCCTAAAGTCAA+AGG - chr4.4:86693973-86693992 None:intergenic 50.0%
ACTGGGGGCCTAAAGTCAAA+GGG - chr4.4:86693972-86693991 None:intergenic 50.0%
AGGGAAATGCCTGTTGTTGG+TGG + chr4.4:86694150-86694169 MS.gene068294:CDS 50.0%
AGTCCACTACCACCAACAAC+AGG - chr4.4:86694162-86694181 None:intergenic 50.0%
CAAGCTTGGAACTCAACTGG+GGG - chr4.4:86693987-86694006 None:intergenic 50.0%
!! ATGCCTGTTGTTGGTGGTAG+TGG + chr4.4:86694156-86694175 MS.gene068294:CDS 50.0%


Chromosome Type Strat End Strand Name
chr4.4 gene 86693694 86694284 86693694 ID=MS.gene068294
chr4.4 mRNA 86693694 86694284 86693694 ID=MS.gene068294.t1;Parent=MS.gene068294
chr4.4 exon 86693694 86694284 86693694 ID=MS.gene068294.t1.exon1;Parent=MS.gene068294.t1
chr4.4 CDS 86693694 86694284 86693694 ID=cds.MS.gene068294.t1;Parent=MS.gene068294.t1
Gene Sequence

>MS.gene068294

ATGTCTTCCAAACATTTTCTCACTTTGTTCTTCTTCCTTCTCATCTCTTGCAACAAACTCACTGCTTCAACTTCATCAGAAAATCAAGACGTTGATTTTGTTCGTCAAATAGATCGCAAGTTGTTAGGCCTAAACAAGAAGGAAAAGCTAAGTCATTTCAAATTATATTGGCATGACATAATTAGTGGAAAAAATCCAACTTCGGTTGCAATTGTTCCACCATCATCAAAAGTAAACTCAACTACTTTTTTTGGTTTCGTCAACATGATTGACAACCCTTTGACTTTAGGCCCCCAGTTGAGTTCCAAGCTTGTTGGAAAAGCTCAAGGTTTCTATGCATCTGCATCACAGGAAGAAATAGGTTTTCTTATGATAATGAATTTTGCTTTCACTGAAGGAAAGTATAATGGGAGTACTATTACTATCTTGGGGAGGAATCCTGCTTTTAATAAGGTTAGGGAAATGCCTGTTGTTGGTGGTAGTGGACTTTTTAGATTTGCTAGAGGATATGCTCAAGCTAGTACTCATTGGATTGATGTCAAAGCTCGGGATGCTTGTGTTGAGTACAATGTGTATGTTTTTCACTATTGA
Protein sequence

>MS.gene068294.t1

MSSKHFLTLFFFLLISCNKLTASTSSENQDVDFVRQIDRKLLGLNKKEKLSHFKLYWHDIISGKNPTSVAIVPPSSKVNSTTFFGFVNMIDNPLTLGPQLSSKLVGKAQGFYASASQEEIGFLMIMNFAFTEGKYNGSTITILGRNPAFNKVREMPVVGGSGLFRFARGYAQASTHWIDVKARDACVEYNVYVFHY