AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1397680

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1397680 MtrunA17_Chr7g0218151 91.824 159 13 0 1 159 1 159 2.57e-98 280
Msa1397680 MtrunA17_Chr4g0012761 90.566 159 15 0 1 159 1 159 2.52e-95 272
Msa1397680 MtrunA17_Chr1g0188661 83.648 159 26 0 1 159 1 159 3.05e-88 254
Msa1397680 MtrunA17_Chr5g0420351 69.872 156 47 0 1 156 1 156 4.51e-75 221
Msa1397680 MtrunA17_Chr1g0188681 68.790 157 49 0 1 157 1 157 7.22e-74 218
Msa1397680 MtrunA17_Chr1g0193311 75.000 156 39 0 1 156 1 156 2.00e-73 217
Msa1397680 MtrunA17_Chr1g0188651 74.843 159 38 1 1 159 1 157 9.37e-73 215
Msa1397680 MtrunA17_Chr1g0197261 53.548 155 72 0 1 155 1 155 7.23e-56 172
Msa1397680 MtrunA17_Chr1g0197461 55.556 153 68 0 3 155 2 154 1.25e-55 172
Msa1397680 MtrunA17_Chr1g0197321 51.282 156 75 1 1 155 1 156 2.29e-53 166
Msa1397680 MtrunA17_Chr3g0107381 45.752 153 82 1 1 152 1 153 3.37e-41 137
Msa1397680 MtrunA17_Chr4g0014321 40.645 155 90 2 1 153 1 155 1.25e-40 136
Msa1397680 MtrunA17_Chr3g0110131 48.408 157 80 1 1 156 1 157 7.22e-39 132
Msa1397680 MtrunA17_Chr4g0013041 39.103 156 91 3 1 154 1 154 3.65e-36 124
Msa1397680 MtrunA17_Chr5g0432691 36.538 156 98 1 1 155 1 156 1.93e-34 118
Msa1397680 MtrunA17_Chr3g0107351 42.857 154 87 1 3 155 2 155 3.15e-34 117
Msa1397680 MtrunA17_Chr3g0107331 42.038 157 90 1 3 158 2 158 3.71e-34 117
Msa1397680 MtrunA17_Chr8g0351751 40.252 159 91 2 1 155 1 159 5.47e-34 119
Msa1397680 MtrunA17_Chr3g0107361 40.260 154 91 1 3 155 2 155 1.74e-31 110
Msa1397680 MtrunA17_Chr3g0107341 40.260 154 91 1 3 155 2 155 3.92e-31 110
Msa1397680 MtrunA17_Chr3g0107461 35.220 159 101 2 1 157 1 159 5.33e-30 107
Msa1397680 MtrunA17_Chr4g0014031 41.333 150 86 2 1 148 1 150 6.23e-30 108
Msa1397680 MtrunA17_Chr2g0283941 38.994 159 95 2 1 157 1 159 1.40e-29 108
Msa1397680 MtrunA17_Chr4g0014121 41.250 160 92 2 1 158 29 188 6.72e-29 105
Msa1397680 MtrunA17_Chr4g0014131 38.509 161 97 2 1 159 1 161 1.50e-26 100
Msa1397680 MtrunA17_Chr2g0296861 35.484 155 99 1 1 154 1 155 5.73e-25 94.0
Msa1397680 MtrunA17_Chr2g0296831 41.525 118 68 1 1 117 1 118 9.38e-24 89.7
Msa1397680 MtrunA17_Chr4g0031421 32.824 131 86 2 29 157 1 131 1.59e-19 79.7
Msa1397680 MtrunA17_Chr3g0105791 33.588 131 85 2 29 157 1 131 2.63e-19 79.0
Msa1397680 MtrunA17_Chr4g0008701 36.800 125 71 4 1 121 1 121 6.03e-17 77.0
Msa1397680 MtrunA17_Chr7g0267601 33.333 114 72 2 3 115 6 116 2.64e-16 75.1
Msa1397680 MtrunA17_Chr3g0106421 33.846 130 82 3 29 155 1 129 5.70e-16 72.0
Msa1397680 MtrunA17_Chr3g0106501 32.061 131 87 2 29 157 1 131 1.13e-14 67.4
Msa1397680 MtrunA17_Chr6g0449861 35.789 95 55 3 1 89 9 103 2.40e-13 66.2
Msa1397680 MtrunA17_Chr1g0161931 43.617 94 52 1 64 156 28 121 3.17e-13 62.8
Msa1397680 MtrunA17_Chr1g0162261 39.796 98 58 1 62 158 20 117 5.61e-13 62.0
Msa1397680 MtrunA17_Chr6g0457851 35.000 80 46 3 1 74 11 90 1.14e-12 64.3
Msa1397680 MtrunA17_Chr3g0128721 30.973 113 76 1 3 115 6 116 3.82e-12 63.2
Msa1397680 MtrunA17_Chr1g0162181 37.168 113 64 2 53 158 5 117 6.47e-12 59.3
Msa1397680 MtrunA17_Chr1g0212151 33.750 80 47 2 1 74 1 80 7.47e-12 62.0
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1397680 AT5G48670.1 47.712 153 79 1 1 152 1 153 9.82e-36 126
Msa1397680 AT3G05860.2 40.940 149 87 1 1 148 1 149 1.11e-33 118
Msa1397680 AT3G05860.3 40.940 149 87 1 1 148 1 149 7.46e-33 117
Msa1397680 AT3G05860.1 40.940 149 87 1 1 148 1 149 1.01e-32 117
Msa1397680 AT5G26630.1 39.375 160 96 1 1 159 1 160 1.06e-28 105
Msa1397680 AT1G65300.1 37.324 142 88 1 3 143 2 143 1.41e-27 104
Msa1397680 AT1G65330.1 37.415 147 91 1 3 148 2 148 5.44e-27 102
Msa1397680 AT5G26650.1 35.294 153 98 1 4 155 2 154 3.75e-25 99.4
Msa1397680 AT5G27960.1 34.641 153 99 1 4 155 2 154 6.33e-24 95.5
Msa1397680 AT5G27810.1 44.792 96 52 1 29 123 1 96 2.65e-22 86.3
Msa1397680 AT1G22590.2 41.304 92 47 1 1 85 1 92 1.85e-21 85.5
Msa1397680 AT2G28700.1 32.886 149 99 1 1 148 1 149 1.94e-21 89.0
Msa1397680 AT1G31630.1 29.677 155 107 2 3 156 2 155 3.80e-21 88.2
Msa1397680 AT1G31640.1 32.000 150 100 2 3 151 2 150 4.20e-19 83.2
Msa1397680 AT5G26580.1 32.903 155 91 1 1 155 1 142 1.05e-17 79.0
Msa1397680 AT5G06500.1 30.818 159 106 3 1 157 1 157 6.26e-15 70.1
Msa1397680 AT2G40210.1 38.835 103 58 2 1 100 1 101 9.06e-15 70.9
Msa1397680 AT5G58890.1 37.500 96 53 2 1 89 1 96 2.07e-14 69.3
Msa1397680 AT5G55690.1 35.802 81 45 2 1 74 1 81 8.59e-12 62.0
Msa1397680 AT5G55690.2 35.802 81 45 2 1 74 1 81 8.59e-12 62.0

Find 26 sgRNAs with CRISPR-Local

Find 25 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CTCCTTTCTTGTTGAATCAT+TGG 0.233760 tig0022176:+29178 None:intergenic
TGTTGAATCATTGGAAATAA+AGG 0.251603 tig0022176:+29187 None:intergenic
AGCAGAACATTCTTATGTTT+TGG 0.267458 tig0022176:-28881 Msa1397680:CDS
ACCTTTCTTCCTCCTCTTGT+AGG 0.274122 tig0022176:+29154 None:intergenic
TGTTTGGCTTCCTTTAGATT+TGG 0.353502 tig0022176:+29038 None:intergenic
ATACCTCTCAATCACCTGTT+TGG 0.354870 tig0022176:+29022 None:intergenic
TTCCAATGATTCAACAAGAA+AGG 0.389550 tig0022176:-29180 Msa1397680:CDS
TTTGCAAAAGGAAACTTTCT+CGG 0.420759 tig0022176:+28961 None:intergenic
AAATCTAAAGGAAGCCAAAC+AGG 0.425294 tig0022176:-29036 Msa1397680:CDS
TCAGAAACAGTCACATCATC+TGG 0.447805 tig0022176:+28837 None:intergenic
CTTTAGTAATCATTTGCAAA+AGG 0.449651 tig0022176:+28949 None:intergenic
ACCTACAAGAGGAGGAAGAA+AGG 0.464332 tig0022176:-29155 Msa1397680:CDS
TGTTTCTGATTTGAAAGACT+TGG 0.473410 tig0022176:-28823 Msa1397680:CDS
TTTCACCTTCTTCCTAGTCA+TGG 0.490416 tig0022176:+29214 None:intergenic
GCAAATGATTACTAAAGCTA+CGG 0.498143 tig0022176:-28943 Msa1397680:CDS
ACCTCTGTTTCAGAATCAAA+AGG 0.516061 tig0022176:+29065 None:intergenic
AGAGGTGTGGCCAAATCTAA+AGG 0.522555 tig0022176:-29048 Msa1397680:CDS
AGAGAACTCACTATTCTTTG+TGG 0.526508 tig0022176:-29116 Msa1397680:CDS
CAAAGCCATGACTAGGAAGA+AGG 0.543154 tig0022176:-29219 None:intergenic
GAAGGAAATTGATGACAAGA+TGG 0.549956 tig0022176:-28778 Msa1397680:CDS
GAAAGGAGACCTACAAGAGG+AGG 0.585792 tig0022176:-29163 Msa1397680:CDS
GAAGAAAGGTATCATCAAGA+AGG 0.595296 tig0022176:-29141 Msa1397680:CDS
TACATTGCAAAGCCATGACT+AGG 0.609749 tig0022176:-29226 None:intergenic
TTGATTCTGAAACAGAGGTG+TGG 0.630350 tig0022176:-29061 Msa1397680:CDS
AAGCCAAACAGGTGATTGAG+AGG 0.637552 tig0022176:-29025 Msa1397680:CDS
CAAGAAAGGAGACCTACAAG+AGG 0.685284 tig0022176:-29166 Msa1397680:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! GTTAATTGAAAAAAATATGA+AGG - tig0022176:29171-29190 Msa1397680:CDS 15.0%
! TGTTGAATCATTGGAAATAA+AGG + tig0022176:28783-28802 None:intergenic 25.0%
! CTTTAGTAATCATTTGCAAA+AGG + tig0022176:29021-29040 None:intergenic 25.0%
TTCCAATGATTCAACAAGAA+AGG - tig0022176:28787-28806 Msa1397680:CDS 30.0%
TTTGCAAAAGGAAACTTTCT+CGG + tig0022176:29009-29028 None:intergenic 30.0%
GCAAATGATTACTAAAGCTA+CGG - tig0022176:29024-29043 Msa1397680:CDS 30.0%
! AGCAGAACATTCTTATGTTT+TGG - tig0022176:29086-29105 Msa1397680:CDS 30.0%
! TGTTTCTGATTTGAAAGACT+TGG - tig0022176:29144-29163 Msa1397680:CDS 30.0%
CTCCTTTCTTGTTGAATCAT+TGG + tig0022176:28792-28811 None:intergenic 35.0%
!! GAAGAAAGGTATCATCAAGA+AGG - tig0022176:28826-28845 Msa1397680:CDS 35.0%
AGAGAACTCACTATTCTTTG+TGG - tig0022176:28851-28870 Msa1397680:CDS 35.0%
!!! TCCTTTTGATTCTGAAACAG+AGG - tig0022176:28901-28920 Msa1397680:CDS 35.0%
ACCTCTGTTTCAGAATCAAA+AGG + tig0022176:28905-28924 None:intergenic 35.0%
! TGTTTGGCTTCCTTTAGATT+TGG + tig0022176:28932-28951 None:intergenic 35.0%
AAATCTAAAGGAAGCCAAAC+AGG - tig0022176:28931-28950 Msa1397680:CDS 35.0%
! GAAGGAAATTGATGACAAGA+TGG - tig0022176:29189-29208 Msa1397680:CDS 35.0%
!! TTGATTCTGAAACAGAGGTG+TGG - tig0022176:28906-28925 Msa1397680:CDS 40.0%
ATACCTCTCAATCACCTGTT+TGG + tig0022176:28948-28967 None:intergenic 40.0%
TCAGAAACAGTCACATCATC+TGG + tig0022176:29133-29152 None:intergenic 40.0%
CAAGAAAGGAGACCTACAAG+AGG - tig0022176:28801-28820 Msa1397680:CDS 45.0%
ACCTACAAGAGGAGGAAGAA+AGG - tig0022176:28812-28831 Msa1397680:CDS 45.0%
ACCTTTCTTCCTCCTCTTGT+AGG + tig0022176:28816-28835 None:intergenic 45.0%
! AGAGGTGTGGCCAAATCTAA+AGG - tig0022176:28919-28938 Msa1397680:CDS 45.0%
AAGCCAAACAGGTGATTGAG+AGG - tig0022176:28942-28961 Msa1397680:CDS 45.0%
GAAAGGAGACCTACAAGAGG+AGG - tig0022176:28804-28823 Msa1397680:CDS 50.0%
Chromosome Type Strat End Strand Name
tig0022176 gene 28755 29234 28755 ID=Msa1397680;Name=Msa1397680
tig0022176 mRNA 28755 29234 28755 ID=Msa1397680-mRNA-1;Parent=Msa1397680;Name=Msa1397680-mRNA-1;_AED=0.00;_eAED=0.00;_QI=0|-1|0|1|-1|1|1|0|159
tig0022176 exon 28755 29234 28755 ID=Msa1397680-mRNA-1:exon:16257;Parent=Msa1397680-mRNA-1
tig0022176 CDS 28755 29234 28755 ID=Msa1397680-mRNA-1:cds;Parent=Msa1397680-mRNA-1
Gene Sequence

>Msa1397680

ATGACTAGGAAGAAGGTGAAACTCGCCTTTATTTCCAATGATTCAACAAGAAAGGAGACCTACAAGAGGAGGAAGAAAGGTATCATCAAGAAGGTGAGAGAACTCACTATTCTTTGTGGTATTTCAGCATGTGCTATAATTTATGATCCTTTTGATTCTGAAACAGAGGTGTGGCCAAATCTAAAGGAAGCCAAACAGGTGATTGAGAGGTATCAAAACTCATATATGAAAGATGAGAGAAAAAATGTGAACCGAGAAAGTTTCCTTTTGCAAATGATTACTAAAGCTACGGAACAACTGAGAATGCAAAGACACGACAATCATGAGAATGAGCAGAACATTCTTATGTTTTGGTACATGCAAAACAACAAGCTGCCAGATGATGTGACTGTTTCTGATTTGAAAGACTTGGATAAGTTAATTGAAAAAAATATGAAGGAAATTGATGACAAGATGGCTTCACTTAGTTTATCAAACTGA
Protein sequence

>Msa1397680

MTRKKVKLAFISNDSTRKETYKRRKKGIIKKVRELTILCGISACAIIYDPFDSETEVWPNLKEAKQVIERYQNSYMKDERKNVNRESFLLQMITKATEQLRMQRHDNHENEQNILMFWYMQNNKLPDDVTVSDLKDLDKLIEKNMKEIDDKMASLSLSN*