AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0585160

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0585160 MtrunA17_Chr4g0014031 72.650 234 47 2 1 222 1 229 3.72e-113 323
Msa0585160 MtrunA17_Chr4g0014131 70.492 244 37 2 1 222 1 231 3.91e-110 315
Msa0585160 MtrunA17_Chr4g0014321 58.874 231 86 1 1 222 1 231 9.29e-97 281
Msa0585160 MtrunA17_Chr8g0351751 59.109 247 76 4 1 222 1 247 1.16e-91 269
Msa0585160 MtrunA17_Chr4g0013041 63.077 195 64 2 1 195 1 187 2.75e-87 256
Msa0585160 MtrunA17_Chr4g0014121 80.892 157 30 0 1 157 29 185 9.62e-83 244
Msa0585160 MtrunA17_Chr3g0110131 48.963 241 98 4 1 219 1 238 1.00e-64 200
Msa0585160 MtrunA17_Chr3g0107381 46.018 226 108 3 1 222 1 216 4.77e-63 195
Msa0585160 MtrunA17_Chr2g0296831 72.951 122 33 0 1 122 1 122 1.21e-51 163
Msa0585160 MtrunA17_Chr3g0107331 47.020 151 79 1 3 153 2 151 1.71e-44 146
Msa0585160 MtrunA17_Chr5g0432691 45.806 155 83 1 1 155 1 154 2.26e-44 145
Msa0585160 MtrunA17_Chr3g0107461 42.308 156 90 0 1 156 1 156 2.23e-42 140
Msa0585160 MtrunA17_Chr5g0420351 44.872 156 84 2 1 156 1 154 1.83e-41 138
Msa0585160 MtrunA17_Chr3g0107351 44.737 152 83 1 3 154 2 152 2.03e-41 138
Msa0585160 MtrunA17_Chr2g0283941 38.983 177 107 1 1 176 1 177 3.06e-40 138
Msa0585160 MtrunA17_Chr3g0107361 42.763 152 86 1 3 154 2 152 6.17e-39 132
Msa0585160 MtrunA17_Chr3g0107341 44.079 152 84 1 3 154 2 152 9.31e-39 131
Msa0585160 MtrunA17_Chr1g0188681 41.667 156 89 2 1 156 1 154 9.32e-39 131
Msa0585160 MtrunA17_Chr1g0188661 44.231 156 85 2 1 156 1 154 1.04e-35 124
Msa0585160 MtrunA17_Chr1g0197461 40.260 154 90 2 3 156 2 153 2.55e-35 122
Msa0585160 MtrunA17_Chr7g0218151 43.590 156 86 2 1 156 1 154 3.03e-35 122
Msa0585160 MtrunA17_Chr3g0105791 43.651 126 71 0 29 154 1 126 1.58e-34 120
Msa0585160 MtrunA17_Chr4g0012761 42.949 156 87 2 1 156 1 154 3.74e-34 119
Msa0585160 MtrunA17_Chr1g0188651 43.590 156 84 2 1 156 1 152 6.96e-34 119
Msa0585160 MtrunA17_Chr1g0197261 40.667 150 87 2 1 150 1 148 1.13e-33 118
Msa0585160 MtrunA17_Chr1g0197321 38.312 154 94 1 1 154 1 153 1.37e-33 118
Msa0585160 MtrunA17_Chr1g0193311 43.590 156 86 2 1 156 1 154 1.92e-33 117
Msa0585160 MtrunA17_Chr4g0031421 43.651 126 71 0 29 154 1 126 3.24e-33 117
Msa0585160 MtrunA17_Chr3g0106421 34.197 193 115 4 29 216 1 186 8.00e-32 115
Msa0585160 MtrunA17_Chr2g0296861 36.306 157 99 1 1 157 1 156 2.35e-25 97.1
Msa0585160 MtrunA17_Chr7g0267601 39.370 127 77 0 3 129 6 132 5.98e-25 102
Msa0585160 MtrunA17_Chr4g0008701 40.157 127 76 0 3 129 6 132 6.90e-25 101
Msa0585160 MtrunA17_Chr3g0128721 36.364 132 83 1 3 133 6 137 2.89e-22 94.4
Msa0585160 MtrunA17_Chr2g0296851 61.728 81 31 0 74 154 1 81 3.50e-21 84.3
Msa0585160 MtrunA17_Chr3g0106501 32.031 128 87 0 29 156 1 128 5.85e-20 82.8
Msa0585160 MtrunA17_Chr6g0457851 35.398 113 66 4 1 107 11 122 1.42e-13 68.9
Msa0585160 MtrunA17_Chr6g0449861 35.398 113 66 4 1 107 9 120 1.70e-13 68.6
Msa0585160 MtrunA17_Chr1g0212151 32.743 113 69 3 1 107 1 112 2.98e-13 67.8
Msa0585160 MtrunA17_Chr6g0449851 36.283 113 65 4 1 107 1 112 2.75e-11 62.0
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0585160 AT5G48670.1 54.545 154 69 1 1 154 1 153 2.68e-46 156
Msa0585160 AT1G65300.1 42.857 168 86 2 3 161 2 168 1.83e-41 142
Msa0585160 AT5G26630.1 42.927 205 106 2 1 195 1 204 4.14e-41 139
Msa0585160 AT1G65330.1 43.452 168 87 2 3 163 2 168 3.57e-40 139
Msa0585160 AT5G26650.1 43.421 152 85 1 5 156 3 153 8.43e-37 132
Msa0585160 AT5G27960.1 42.262 168 85 5 5 161 3 169 4.22e-36 129
Msa0585160 AT1G31630.1 37.500 168 96 3 3 163 2 167 1.10e-35 129
Msa0585160 AT1G31640.1 39.073 151 90 2 3 153 2 150 3.17e-32 122
Msa0585160 AT2G28700.1 36.723 177 107 2 1 175 1 174 1.43e-31 118
Msa0585160 AT5G27810.1 55.914 93 41 0 29 121 1 93 1.67e-31 112
Msa0585160 AT3G05860.2 36.709 158 99 1 1 158 1 157 1.17e-30 112
Msa0585160 AT3G05860.3 36.709 158 99 1 1 158 1 157 3.37e-30 112
Msa0585160 AT3G05860.1 36.709 158 99 1 1 158 1 157 3.63e-30 112
Msa0585160 AT5G26580.1 35.714 154 84 2 1 154 1 139 2.82e-25 101
Msa0585160 AT1G22590.2 31.481 162 107 1 1 162 1 158 4.02e-25 97.1
Msa0585160 AT5G06500.1 35.032 157 100 2 1 157 1 155 1.27e-21 89.7
Msa0585160 AT2G40210.1 40.310 129 76 1 1 129 1 128 4.78e-20 87.4
Msa0585160 AT5G58890.1 38.583 127 67 5 6 123 6 130 1.51e-16 77.0
Msa0585160 AT5G55690.1 42.308 78 38 2 1 71 1 78 1.84e-13 68.2
Msa0585160 AT5G55690.2 42.308 78 38 2 1 71 1 78 1.84e-13 68.2
Msa0585160 AT2G15660.1 30.973 113 73 2 38 150 31 138 9.32e-12 63.2
Msa0585160 AT5G27090.1 28.221 163 95 6 7 164 23 168 5.09e-11 60.1

Find 61 sgRNAs with CRISPR-Local

Find 60 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ATCCTTCAAGGTAGTAAATT+AGG 0.161446 4_2:-5687532 None:intergenic
AGAAACAAAGAAAAGAAAAT+AGG 0.231520 4_2:+5687185 Msa0585160:CDS
CCCTTTGGTGAGATCAATTA+TGG 0.234667 4_2:+5687502 Msa0585160:CDS
GAGCGAAGAAATGGCAATTA+TGG 0.251384 4_2:+5687381 Msa0585160:CDS
TACCAATGTCCTTCAAATTA+TGG 0.254451 4_2:-5687312 None:intergenic
AAGAAAGGGTCTATTGAAAA+AGG 0.312767 4_2:+5686952 Msa0585160:CDS
ATCTCTGGCTGAGGCTCATA+AGG 0.350996 4_2:-5687028 None:intergenic
AAAATGTCATCACCATTAAT+AGG 0.355958 4_2:-5687424 None:intergenic
ATGAGCCTCAGCCAGAGATT+TGG 0.374512 4_2:+5687032 Msa0585160:CDS
TTTGCAAAGTCAATTATTGA+TGG 0.379269 4_2:+5687444 Msa0585160:CDS
GCCCTAATTTACTACCTTGA+AGG 0.380748 4_2:+5687530 Msa0585160:CDS
TCCTTCAAGGTAGTAAATTA+GGG 0.396741 4_2:-5687531 None:intergenic
GAAGGACATTGGTAGACGTT+TGG 0.410243 4_2:+5687321 Msa0585160:CDS
TCTGGTGAAGGCCAAATCTC+TGG 0.413104 4_2:-5687043 None:intergenic
GAAACAAAGAAAAGAAAATA+GGG 0.419680 4_2:+5687186 Msa0585160:CDS
AGCGAAGAAATGGCAATTAT+GGG 0.425600 4_2:+5687382 Msa0585160:CDS
AGCATCTAGGAGCGAAGAAA+TGG 0.428793 4_2:+5687372 Msa0585160:CDS
GTTGATTGACCATAATTTGA+AGG 0.445081 4_2:+5687303 Msa0585160:CDS
GATGCTGCTGGAGGTGGTAG+TGG 0.453710 4_2:-5687355 None:intergenic
CTCCTAGATGCTGCTGGAGG+TGG 0.459401 4_2:-5687361 None:intergenic
CACAACCATGGCTAGAAGTA+AGG 0.461347 4_2:+5686874 None:intergenic
CTCATAAGGGCCATACACTA+TGG 0.468858 4_2:-5687014 None:intergenic
ATCATACAAGAAAAGAAGAA+AGG 0.473094 4_2:+5686937 Msa0585160:CDS
CTTGACACAAAGGGTTCTGA+AGG 0.478789 4_2:+5687147 Msa0585160:CDS
TCAATTATTGATGGACTCAA+TGG 0.482426 4_2:+5687453 Msa0585160:CDS
CATGTTGGGATACCTATTAA+TGG 0.485702 4_2:+5687412 Msa0585160:CDS
TCTTCGCTCCTAGATGCTGC+TGG 0.487238 4_2:-5687367 None:intergenic
TTGATTTGAGTTATCTTACT+TGG 0.491177 4_2:+5687281 Msa0585160:CDS
TTATGGGTCATGGACATGTT+GGG 0.500968 4_2:+5687398 Msa0585160:CDS
TGCGGCATCATTGACAATGA+AGG 0.507200 4_2:-5686906 None:intergenic
ATTATGGGTCATGGACATGT+TGG 0.516074 4_2:+5687397 Msa0585160:CDS
AGAGACTTTCTTGACACAAA+GGG 0.517022 4_2:+5687138 Msa0585160:CDS
GACCATAATTTGAAGGACAT+TGG 0.517963 4_2:+5687310 Msa0585160:CDS
GAAATGGCAATTATGGGTCA+TGG 0.521926 4_2:+5687388 Msa0585160:CDS
GGACATTGGTAGACGTTTGG+CGG 0.524285 4_2:+5687324 Msa0585160:CDS
TTTGTGTCAAGAAAGTCTCT+TGG 0.525855 4_2:-5687135 None:intergenic
TCATACAAGAAAAGAAGAAA+GGG 0.526600 4_2:+5686938 Msa0585160:CDS
TTTAACCTTACTTCTAGCCA+TGG 0.533701 4_2:-5686879 None:intergenic
TACCACCTCCAGCAGCATCT+AGG 0.540428 4_2:+5687359 Msa0585160:CDS
ATGTCTCATTGTCTCAATGA+AGG 0.542205 4_2:+5687229 Msa0585160:CDS
GTGCAAGAGACAGTGCCCTT+TGG 0.557727 4_2:+5687487 Msa0585160:CDS
CCATAATTGATCTCACCAAA+GGG 0.558369 4_2:-5687502 None:intergenic
GAAGCCTGTGCCATAGTGTA+TGG 0.559714 4_2:+5687004 Msa0585160:CDS
GAAGGCCAAATCTCTGGCTG+AGG 0.560020 4_2:-5687037 None:intergenic
TCTCTGGCTGAGGCTCATAA+GGG 0.571102 4_2:-5687027 None:intergenic
GAGATTTGGCCTTCACCAGA+GGG 0.580805 4_2:+5687046 Msa0585160:CDS
TCCATAATTGATCTCACCAA+AGG 0.580970 4_2:-5687503 None:intergenic
ACAGGCTTCAATGCCACAGA+GGG 0.601811 4_2:-5686990 None:intergenic
GATTTGGCCTTCACCAGAGG+GGG 0.601928 4_2:+5687048 Msa0585160:CDS
CTTGTATGATTCTTTCCTTG+CGG 0.605657 4_2:-5686924 None:intergenic
TTGATGGACTCAATGGTGGC+TGG 0.607204 4_2:+5687460 Msa0585160:CDS
AAGAGACTTTCTTGACACAA+AGG 0.607804 4_2:+5687137 Msa0585160:CDS
AGAGATTTGGCCTTCACCAG+AGG 0.617598 4_2:+5687045 Msa0585160:CDS
TGTGCACGACAATATGTCAA+TGG 0.625522 4_2:+5687258 Msa0585160:CDS
AGGGCCATACACTATGGCAC+AGG 0.641363 4_2:-5687008 None:intergenic
TCATTGTCAATGATGCCGCA+AGG 0.664783 4_2:+5686909 Msa0585160:CDS
ATTATTGATGGACTCAATGG+TGG 0.666274 4_2:+5687456 Msa0585160:CDS
TCGCTCCTAGATGCTGCTGG+AGG 0.676090 4_2:-5687364 None:intergenic
GCTGAACTTAGCACCCTCTG+TGG 0.677042 4_2:+5686977 Msa0585160:CDS
CACAGGCTTCAATGCCACAG+AGG 0.696692 4_2:-5686991 None:intergenic
AGATTTGGCCTTCACCAGAG+GGG 0.703414 4_2:+5687047 Msa0585160:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AGAAACAAAGAAAAGAAAAT+AGG + chr4_2:5687185-5687204 Msa0585160:CDS 20.0%
!! GAAACAAAGAAAAGAAAATA+GGG + chr4_2:5687186-5687205 Msa0585160:CDS 20.0%
! ATCATACAAGAAAAGAAGAA+AGG + chr4_2:5686937-5686956 Msa0585160:CDS 25.0%
! TCATACAAGAAAAGAAGAAA+GGG + chr4_2:5686938-5686957 Msa0585160:CDS 25.0%
!! TTGATTTGAGTTATCTTACT+TGG + chr4_2:5687281-5687300 Msa0585160:CDS 25.0%
! AAAATGTCATCACCATTAAT+AGG - chr4_2:5687427-5687446 None:intergenic 25.0%
! TTTGCAAAGTCAATTATTGA+TGG + chr4_2:5687444-5687463 Msa0585160:CDS 25.0%
AAGAAAGGGTCTATTGAAAA+AGG + chr4_2:5686952-5686971 Msa0585160:CDS 30.0%
GTTGATTGACCATAATTTGA+AGG + chr4_2:5687303-5687322 Msa0585160:CDS 30.0%
TACCAATGTCCTTCAAATTA+TGG - chr4_2:5687315-5687334 None:intergenic 30.0%
!! TCAATTATTGATGGACTCAA+TGG + chr4_2:5687453-5687472 Msa0585160:CDS 30.0%
CTTGTATGATTCTTTCCTTG+CGG - chr4_2:5686927-5686946 None:intergenic 35.0%
TTTGTGTCAAGAAAGTCTCT+TGG - chr4_2:5687138-5687157 None:intergenic 35.0%
AAGAGACTTTCTTGACACAA+AGG + chr4_2:5687137-5687156 Msa0585160:CDS 35.0%
AGAGACTTTCTTGACACAAA+GGG + chr4_2:5687138-5687157 Msa0585160:CDS 35.0%
ATGTCTCATTGTCTCAATGA+AGG + chr4_2:5687229-5687248 Msa0585160:CDS 35.0%
GACCATAATTTGAAGGACAT+TGG + chr4_2:5687310-5687329 Msa0585160:CDS 35.0%
AGCGAAGAAATGGCAATTAT+GGG + chr4_2:5687382-5687401 Msa0585160:CDS 35.0%
CATGTTGGGATACCTATTAA+TGG + chr4_2:5687412-5687431 Msa0585160:CDS 35.0%
!! ATTATTGATGGACTCAATGG+TGG + chr4_2:5687456-5687475 Msa0585160:CDS 35.0%
CCATAATTGATCTCACCAAA+GGG - chr4_2:5687505-5687524 None:intergenic 35.0%
TCCATAATTGATCTCACCAA+AGG - chr4_2:5687506-5687525 None:intergenic 35.0%
!! TGAATTTTGAGAGCACGGAT+TGG - chr4_2:5687075-5687094 None:intergenic 40.0%
!! CGTCATGAATTTTGAGAGCA+CGG - chr4_2:5687080-5687099 None:intergenic 40.0%
TGTGCACGACAATATGTCAA+TGG + chr4_2:5687258-5687277 Msa0585160:CDS 40.0%
GAGCGAAGAAATGGCAATTA+TGG + chr4_2:5687381-5687400 Msa0585160:CDS 40.0%
GAAATGGCAATTATGGGTCA+TGG + chr4_2:5687388-5687407 Msa0585160:CDS 40.0%
ATTATGGGTCATGGACATGT+TGG + chr4_2:5687397-5687416 Msa0585160:CDS 40.0%
TTATGGGTCATGGACATGTT+GGG + chr4_2:5687398-5687417 Msa0585160:CDS 40.0%
CCCTTTGGTGAGATCAATTA+TGG + chr4_2:5687502-5687521 Msa0585160:CDS 40.0%
TGCGGCATCATTGACAATGA+AGG - chr4_2:5686909-5686928 None:intergenic 45.0%
TCATTGTCAATGATGCCGCA+AGG + chr4_2:5686909-5686928 Msa0585160:CDS 45.0%
CTCATAAGGGCCATACACTA+TGG - chr4_2:5687017-5687036 None:intergenic 45.0%
! CTTGACACAAAGGGTTCTGA+AGG + chr4_2:5687147-5687166 Msa0585160:CDS 45.0%
GAAGGACATTGGTAGACGTT+TGG + chr4_2:5687321-5687340 Msa0585160:CDS 45.0%
AGCATCTAGGAGCGAAGAAA+TGG + chr4_2:5687372-5687391 Msa0585160:CDS 45.0%
ACAGGCTTCAATGCCACAGA+GGG - chr4_2:5686993-5687012 None:intergenic 50.0%
GAAGCCTGTGCCATAGTGTA+TGG + chr4_2:5687004-5687023 Msa0585160:CDS 50.0%
TCTCTGGCTGAGGCTCATAA+GGG - chr4_2:5687030-5687049 None:intergenic 50.0%
ATCTCTGGCTGAGGCTCATA+AGG - chr4_2:5687031-5687050 None:intergenic 50.0%
ATGAGCCTCAGCCAGAGATT+TGG + chr4_2:5687032-5687051 Msa0585160:CDS 50.0%
TCTGGTGAAGGCCAAATCTC+TGG - chr4_2:5687046-5687065 None:intergenic 50.0%
! AGAGATTTGGCCTTCACCAG+AGG + chr4_2:5687045-5687064 Msa0585160:CDS 50.0%
! GAGATTTGGCCTTCACCAGA+GGG + chr4_2:5687046-5687065 Msa0585160:CDS 50.0%
! AGATTTGGCCTTCACCAGAG+GGG + chr4_2:5687047-5687066 Msa0585160:CDS 50.0%
GGACATTGGTAGACGTTTGG+CGG + chr4_2:5687324-5687343 Msa0585160:CDS 50.0%
!! TTGATGGACTCAATGGTGGC+TGG + chr4_2:5687460-5687479 Msa0585160:CDS 50.0%
GCTGAACTTAGCACCCTCTG+TGG + chr4_2:5686977-5686996 Msa0585160:CDS 55.0%
CACAGGCTTCAATGCCACAG+AGG - chr4_2:5686994-5687013 None:intergenic 55.0%
AGGGCCATACACTATGGCAC+AGG - chr4_2:5687011-5687030 None:intergenic 55.0%
GAAGGCCAAATCTCTGGCTG+AGG - chr4_2:5687040-5687059 None:intergenic 55.0%
! GATTTGGCCTTCACCAGAGG+GGG + chr4_2:5687048-5687067 Msa0585160:CDS 55.0%
TACCACCTCCAGCAGCATCT+AGG + chr4_2:5687359-5687378 Msa0585160:CDS 55.0%
TCTTCGCTCCTAGATGCTGC+TGG - chr4_2:5687370-5687389 None:intergenic 55.0%
GTGCAAGAGACAGTGCCCTT+TGG + chr4_2:5687487-5687506 Msa0585160:CDS 55.0%
GATTGGACCCCCTCTGGTGA+AGG - chr4_2:5687058-5687077 None:intergenic 60.0%
GATGCTGCTGGAGGTGGTAG+TGG - chr4_2:5687358-5687377 None:intergenic 60.0%
CTCCTAGATGCTGCTGGAGG+TGG - chr4_2:5687364-5687383 None:intergenic 60.0%
TCGCTCCTAGATGCTGCTGG+AGG - chr4_2:5687367-5687386 None:intergenic 60.0%
!! AGCACGGATTGGACCCCCTC+TGG - chr4_2:5687064-5687083 None:intergenic 65.0%
Chromosome Type Strat End Strand Name
chr4_2 gene 5686881 5687549 5686881 ID=Msa0585160;Name=Msa0585160
chr4_2 mRNA 5686881 5687549 5686881 ID=Msa0585160-mRNA-1;Parent=Msa0585160;Name=Msa0585160-mRNA-1;_AED=0.04;_eAED=0.04;_QI=0|-1|0|1|-1|1|1|0|222
chr4_2 exon 5686881 5687549 5686881 ID=Msa0585160-mRNA-1:exon:1354;Parent=Msa0585160-mRNA-1
chr4_2 CDS 5686881 5687549 5686881 ID=Msa0585160-mRNA-1:cds;Parent=Msa0585160-mRNA-1
Gene Sequence

>Msa0585160

ATGGCTAGAAGTAAGGTTAAACTTGCCTTCATTGTCAATGATGCCGCAAGGAAAGAATCATACAAGAAAAGAAGAAAGGGTCTATTGAAAAAGGTTGCTGAACTTAGCACCCTCTGTGGCATTGAAGCCTGTGCCATAGTGTATGGCCCTTATGAGCCTCAGCCAGAGATTTGGCCTTCACCAGAGGGGGTCCAATCCGTGCTCTCAAAATTCATGACGATGCACGAGTTTCAAAAGTGCAAGAAAATGATGAACCAAGAGACTTTCTTGACACAAAGGGTTCTGAAGGCTGAAGAGAAATTGAAGAAACAAAGAAAAGAAAATAGGGAGCAAGAGATGACAATACTCATGTCTCATTGTCTCAATGAAGGTAGAGTTGTGCACGACAATATGTCAATGGTTGATTTGAGTTATCTTACTTGGTTGATTGACCATAATTTGAAGGACATTGGTAGACGTTTGGCGGCAACAGTGCCACTACCACCTCCAGCAGCATCTAGGAGCGAAGAAATGGCAATTATGGGTCATGGACATGTTGGGATACCTATTAATGGTGATGACATTTTGCAAAGTCAATTATTGATGGACTCAATGGTGGCTGGTAATGTGCAAGAGACAGTGCCCTTTGGTGAGATCAATTATGGAGTTTGCCCTAATTTACTACCTTGA
Protein sequence

>Msa0585160

MARSKVKLAFIVNDAARKESYKKRRKGLLKKVAELSTLCGIEACAIVYGPYEPQPEIWPSPEGVQSVLSKFMTMHEFQKCKKMMNQETFLTQRVLKAEEKLKKQRKENREQEMTILMSHCLNEGRVVHDNMSMVDLSYLTWLIDHNLKDIGRRLAATVPLPPPAASRSEEMAIMGHGHVGIPINGDDILQSQLLMDSMVAGNVQETVPFGEINYGVCPNLLP*