AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0585140

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0585140 MtrunA17_Chr4g0014031 82.645 242 27 1 4 245 3 229 5.25e-137 384
Msa0585140 MtrunA17_Chr4g0014131 80.165 242 35 1 4 245 3 231 2.51e-131 370
Msa0585140 MtrunA17_Chr8g0351751 60.956 251 83 5 4 245 3 247 1.41e-97 285
Msa0585140 MtrunA17_Chr4g0014321 57.959 245 89 4 1 245 1 231 3.84e-94 276
Msa0585140 MtrunA17_Chr4g0014121 81.818 154 28 0 4 157 31 184 4.30e-82 243
Msa0585140 MtrunA17_Chr4g0013041 58.216 213 59 3 6 218 5 187 1.76e-81 243
Msa0585140 MtrunA17_Chr3g0110131 48.133 241 118 3 4 242 3 238 6.62e-63 197
Msa0585140 MtrunA17_Chr3g0107381 54.902 153 68 1 4 156 3 154 7.26e-59 186
Msa0585140 MtrunA17_Chr2g0296831 73.333 120 32 0 4 123 3 122 1.17e-50 161
Msa0585140 MtrunA17_Chr3g0107331 44.720 161 88 1 4 164 2 161 1.70e-44 147
Msa0585140 MtrunA17_Chr3g0107351 43.396 159 89 1 4 162 2 159 9.64e-43 142
Msa0585140 MtrunA17_Chr5g0432691 45.333 150 81 1 6 155 5 153 1.18e-42 142
Msa0585140 MtrunA17_Chr3g0107361 41.509 159 92 1 4 162 2 159 1.60e-40 137
Msa0585140 MtrunA17_Chr3g0107341 42.138 159 91 1 4 162 2 159 5.19e-40 135
Msa0585140 MtrunA17_Chr5g0420351 44.805 154 83 2 4 157 3 154 3.52e-39 133
Msa0585140 MtrunA17_Chr2g0283941 41.447 152 89 0 6 157 5 156 9.89e-39 135
Msa0585140 MtrunA17_Chr3g0107461 40.260 154 92 0 4 157 3 156 2.27e-38 131
Msa0585140 MtrunA17_Chr1g0188681 40.909 154 89 2 4 157 3 154 9.28e-35 122
Msa0585140 MtrunA17_Chr1g0197461 39.610 154 91 2 4 157 2 153 1.07e-34 122
Msa0585140 MtrunA17_Chr1g0197321 39.623 159 94 2 1 159 1 157 2.81e-34 120
Msa0585140 MtrunA17_Chr1g0197261 39.744 156 92 2 4 159 3 156 7.74e-34 119
Msa0585140 MtrunA17_Chr3g0105791 40.146 137 82 0 30 166 1 137 4.19e-33 117
Msa0585140 MtrunA17_Chr7g0218151 42.857 154 86 2 4 157 3 154 2.50e-32 115
Msa0585140 MtrunA17_Chr1g0188661 42.857 154 86 2 4 157 3 154 2.70e-32 115
Msa0585140 MtrunA17_Chr1g0193311 43.506 154 85 2 4 157 3 154 3.01e-32 115
Msa0585140 MtrunA17_Chr4g0031421 40.146 137 82 0 30 166 1 137 3.71e-32 114
Msa0585140 MtrunA17_Chr4g0012761 41.558 154 88 2 4 157 3 154 1.05e-30 111
Msa0585140 MtrunA17_Chr1g0188651 42.138 159 88 2 4 162 3 157 2.47e-29 108
Msa0585140 MtrunA17_Chr3g0106421 40.625 128 76 0 30 157 1 128 1.45e-28 107
Msa0585140 MtrunA17_Chr7g0267601 38.462 156 80 2 3 158 5 144 8.73e-27 107
Msa0585140 MtrunA17_Chr4g0008701 39.103 156 79 2 3 158 5 144 1.09e-26 107
Msa0585140 MtrunA17_Chr3g0128721 29.016 193 126 2 3 195 5 186 4.85e-25 103
Msa0585140 MtrunA17_Chr2g0296851 59.794 97 38 1 75 170 1 97 8.79e-25 94.4
Msa0585140 MtrunA17_Chr2g0296861 35.099 151 97 1 7 157 6 155 5.73e-24 94.0
Msa0585140 MtrunA17_Chr3g0106501 31.538 130 89 0 30 159 1 130 5.04e-19 80.9
Msa0585140 MtrunA17_Chr6g0457851 35.965 114 65 5 1 108 11 122 6.21e-12 64.3
Msa0585140 MtrunA17_Chr6g0449861 35.965 114 65 5 1 108 9 120 6.43e-12 64.3
Msa0585140 MtrunA17_Chr1g0212151 32.432 111 68 3 4 108 3 112 1.31e-11 63.5
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0585140 AT5G48670.1 53.797 158 72 1 4 161 3 159 6.73e-46 155
Msa0585140 AT1G65300.1 45.098 153 83 1 4 156 2 153 5.78e-41 142
Msa0585140 AT1G65330.1 40.541 185 96 2 4 188 2 172 3.58e-39 137
Msa0585140 AT5G26630.1 47.500 160 83 1 4 163 3 161 1.72e-37 131
Msa0585140 AT5G26650.1 40.854 164 96 1 6 169 3 165 4.39e-37 134
Msa0585140 AT5G27960.1 40.244 164 97 1 6 169 3 165 2.48e-36 131
Msa0585140 AT1G31630.1 37.975 158 96 2 4 161 2 157 5.17e-34 125
Msa0585140 AT1G31640.1 39.073 151 90 2 4 154 2 150 7.85e-32 121
Msa0585140 AT5G27810.1 54.839 93 42 0 30 122 1 93 1.30e-30 110
Msa0585140 AT3G05860.2 39.189 148 89 1 4 151 3 149 4.82e-30 111
Msa0585140 AT3G05860.3 39.189 148 89 1 4 151 3 149 1.69e-29 111
Msa0585140 AT3G05860.1 39.189 148 89 1 4 151 3 149 2.02e-29 111
Msa0585140 AT2G28700.1 33.854 192 120 3 4 193 3 189 8.20e-28 108
Msa0585140 AT5G26580.1 36.538 156 83 3 1 156 1 140 4.15e-26 104
Msa0585140 AT1G22590.2 31.847 157 102 2 1 157 1 152 8.95e-25 96.7
Msa0585140 AT5G06500.1 34.868 152 97 2 4 155 3 152 2.59e-19 84.3
Msa0585140 AT2G40210.1 39.098 133 79 2 4 135 3 134 3.09e-17 80.5
Msa0585140 AT5G58890.1 38.583 127 67 5 7 124 6 130 7.07e-16 75.9
Msa0585140 AT5G55690.1 43.750 80 35 4 1 72 1 78 2.85e-12 65.5
Msa0585140 AT5G55690.2 43.750 80 35 4 1 72 1 78 2.85e-12 65.5

Find 61 sgRNAs with CRISPR-Local

Find 61 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AGAAACAAAGAAAAGAAAAT+AGG 0.231520 4_2:+5660140 Msa0585140:CDS
GAGTGAAGAAATGGCAATTA+TGG 0.233693 4_2:+5660402 Msa0585140:CDS
CCATTTCGTGAGGTCAATTC+TGG 0.241200 4_2:+5660523 Msa0585140:CDS
TCAATTTCTCTTCAGCCTTC+AGG 0.259829 4_2:-5660117 None:intergenic
AACGAAGGGTCTATTGAAAA+AGG 0.335070 4_2:+5659907 Msa0585140:CDS
ATGAGCCTCAACCTGAGATT+TGG 0.345571 4_2:+5659987 Msa0585140:CDS
GTGAGGTCAATTCTGGAGTT+TGG 0.368633 4_2:+5660530 Msa0585140:CDS
TTATGGGTCACGGCCATGTT+GGG 0.375329 4_2:+5660419 Msa0585140:CDS
ATAATGTCATCATCATTAAT+AGG 0.375800 4_2:-5660445 None:intergenic
TTGCCATTTCGAGTTGGACT+TGG 0.402057 4_2:-5660345 None:intergenic
TATGCAAAGTCAATTATTGA+TGG 0.408286 4_2:+5660465 Msa0585140:CDS
ATCTCAGGTTGAGGCTCATA+AGG 0.418788 4_2:-5659983 None:intergenic
GAAACAAAGAAAAGAAAATA+GGG 0.419680 4_2:+5660141 Msa0585140:CDS
AGTGAAGAAATGGCAATTAT+GGG 0.424565 4_2:+5660403 Msa0585140:CDS
GAAGGATGTTAGTAGACGTT+TGG 0.425640 4_2:+5660276 Msa0585140:CDS
GGTCTGATTTACTACCTTGA+AGG 0.436579 4_2:+5660551 Msa0585140:CDS
CCAGAATTGACCTCACGAAA+TGG 0.450538 4_2:-5660523 None:intergenic
AAACCAAGTCCAACTCGAAA+TGG 0.452175 4_2:+5660342 Msa0585140:CDS
AGCATCTAGGAGTGAAGAAA+TGG 0.457574 4_2:+5660393 Msa0585140:CDS
AACCTTACTTCTTCTACCCA+TGG 0.464315 4_2:-5659831 None:intergenic
CTCATAAGGTCCATACACTA+TGG 0.479698 4_2:-5659969 None:intergenic
CATCACTTCTAGCAGCATCT+AGG 0.480021 4_2:+5660380 Msa0585140:CDS
TCAATTATTGATGGACTCAA+TGG 0.482426 4_2:+5660474 Msa0585140:CDS
GTTGATTGACCACAATTTGA+AGG 0.487410 4_2:+5660258 Msa0585140:CDS
TCAGGTAAAGGCCAAATCTC+AGG 0.492365 4_2:-5659998 None:intergenic
ATTATGGGTCACGGCCATGT+TGG 0.496223 4_2:+5660418 Msa0585140:CDS
AACCATGGGTAGAAGAAGTA+AGG 0.501192 4_2:+5659829 None:intergenic
TTAGTAGACGTTTGGAAGCA+TGG 0.506023 4_2:+5660284 Msa0585140:CDS
GAGATTTGGCCTTTACCTGA+GGG 0.508411 4_2:+5660001 Msa0585140:CDS
TGGATATGAGTTATCTTGCT+TGG 0.509186 4_2:+5660236 Msa0585140:CDS
TGCAACATCATTGACAATGA+AGG 0.517037 4_2:-5659861 None:intergenic
ATGAGTCAATGTCTTAATGA+AGG 0.517500 4_2:+5660184 Msa0585140:CDS
CAATGATCAAAATCAAATCA+TGG 0.521352 4_2:+5660312 Msa0585140:CDS
TTTGTGTCAAGAAAGTCTCT+TGG 0.525855 4_2:-5660090 None:intergenic
AGAGACTTTCTTGACACAAA+GGG 0.533444 4_2:+5660093 Msa0585140:CDS
GAAGCCTGTGCCATAGTGTA+TGG 0.533456 4_2:+5659959 Msa0585140:CDS
GATTTGGCCTTTACCTGAGG+GGG 0.540882 4_2:+5660003 Msa0585140:CDS
TACTAACATCCTTCAAATTG+TGG 0.547844 4_2:-5660267 None:intergenic
TAGTAGACGTTTGGAAGCAT+GGG 0.553921 4_2:+5660285 Msa0585140:CDS
CTTGACACAAAGGGTCCTGA+AGG 0.570745 4_2:+5660102 Msa0585140:CDS
TTGTTGTTGCCATTTCGAGT+TGG 0.582395 4_2:-5660351 None:intergenic
GAAATGGCAATTATGGGTCA+CGG 0.585455 4_2:+5660409 Msa0585140:CDS
TATGGGTCACGGCCATGTTG+GGG 0.587073 4_2:+5660420 Msa0585140:CDS
TGAGATTTGGCCTTTACCTG+AGG 0.589535 4_2:+5660000 Msa0585140:CDS
CATTAATAGGTACCCCAACA+TGG 0.592472 4_2:-5660432 None:intergenic
CTAGATGCTGCTAGAAGTGA+TGG 0.594440 4_2:-5660379 None:intergenic
TCATTGTCAATGATGTTGCA+AGG 0.595963 4_2:+5659864 Msa0585140:CDS
ACAGGCTTCAATGCCACAGA+GGG 0.601811 4_2:-5659945 None:intergenic
AAAGGCCAAATCTCAGGTTG+AGG 0.605277 4_2:-5659992 None:intergenic
TTGATGGACTCAATGGTGGC+TGG 0.607204 4_2:+5660481 Msa0585140:CDS
ATCATACAAGAAAAGAACGA+AGG 0.618898 4_2:+5659892 Msa0585140:CDS
TCATACAAGAAAAGAACGAA+GGG 0.620354 4_2:+5659893 Msa0585140:CDS
AAGAGACTTTCTTGACACAA+AGG 0.620991 4_2:+5660092 Msa0585140:CDS
AGATTTGGCCTTTACCTGAG+GGG 0.627970 4_2:+5660002 Msa0585140:CDS
AGGTCCATACACTATGGCAC+AGG 0.635258 4_2:-5659963 None:intergenic
AGAGACAGTGCCATTTCGTG+AGG 0.652584 4_2:+5660513 Msa0585140:CDS
ATTATTGATGGACTCAATGG+TGG 0.666274 4_2:+5660477 Msa0585140:CDS
GCATGACAATATGTCAACAA+TGG 0.671130 4_2:+5660216 Msa0585140:CDS
GCTGAACTTAGCACCCTCTG+TGG 0.677042 4_2:+5659932 Msa0585140:CDS
CACAGGCTTCAATGCCACAG+AGG 0.696692 4_2:-5659946 None:intergenic
GATGCTGCTAGAAGTGATGG+TGG 0.726334 4_2:-5660376 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AGAAACAAAGAAAAGAAAAT+AGG + chr4_2:5660140-5660159 Msa0585140:CDS 20.0%
!! GAAACAAAGAAAAGAAAATA+GGG + chr4_2:5660141-5660160 Msa0585140:CDS 20.0%
!! ATAATGTCATCATCATTAAT+AGG - chr4_2:5660448-5660467 None:intergenic 20.0%
! CAATGATCAAAATCAAATCA+TGG + chr4_2:5660312-5660331 Msa0585140:CDS 25.0%
! TATGCAAAGTCAATTATTGA+TGG + chr4_2:5660465-5660484 Msa0585140:CDS 25.0%
ATCATACAAGAAAAGAACGA+AGG + chr4_2:5659892-5659911 Msa0585140:CDS 30.0%
TCATACAAGAAAAGAACGAA+GGG + chr4_2:5659893-5659912 Msa0585140:CDS 30.0%
ATGAGTCAATGTCTTAATGA+AGG + chr4_2:5660184-5660203 Msa0585140:CDS 30.0%
TACTAACATCCTTCAAATTG+TGG - chr4_2:5660270-5660289 None:intergenic 30.0%
AGTGAAGAAATGGCAATTAT+GGG + chr4_2:5660403-5660422 Msa0585140:CDS 30.0%
!! TCAATTATTGATGGACTCAA+TGG + chr4_2:5660474-5660493 Msa0585140:CDS 30.0%
TGCAACATCATTGACAATGA+AGG - chr4_2:5659864-5659883 None:intergenic 35.0%
TCATTGTCAATGATGTTGCA+AGG + chr4_2:5659864-5659883 Msa0585140:CDS 35.0%
AACGAAGGGTCTATTGAAAA+AGG + chr4_2:5659907-5659926 Msa0585140:CDS 35.0%
!! TGAATTTTGAGAGCACAGAT+TGG - chr4_2:5660030-5660049 None:intergenic 35.0%
TTTGTGTCAAGAAAGTCTCT+TGG - chr4_2:5660093-5660112 None:intergenic 35.0%
AAGAGACTTTCTTGACACAA+AGG + chr4_2:5660092-5660111 Msa0585140:CDS 35.0%
AGAGACTTTCTTGACACAAA+GGG + chr4_2:5660093-5660112 Msa0585140:CDS 35.0%
GCATGACAATATGTCAACAA+TGG + chr4_2:5660216-5660235 Msa0585140:CDS 35.0%
TGGATATGAGTTATCTTGCT+TGG + chr4_2:5660236-5660255 Msa0585140:CDS 35.0%
GTTGATTGACCACAATTTGA+AGG + chr4_2:5660258-5660277 Msa0585140:CDS 35.0%
GAGTGAAGAAATGGCAATTA+TGG + chr4_2:5660402-5660421 Msa0585140:CDS 35.0%
!! ATTATTGATGGACTCAATGG+TGG + chr4_2:5660477-5660496 Msa0585140:CDS 35.0%
CTCATAAGGTCCATACACTA+TGG - chr4_2:5659972-5659991 None:intergenic 40.0%
TCAATTTCTCTTCAGCCTTC+AGG - chr4_2:5660120-5660139 None:intergenic 40.0%
GAAGGATGTTAGTAGACGTT+TGG + chr4_2:5660276-5660295 Msa0585140:CDS 40.0%
TTAGTAGACGTTTGGAAGCA+TGG + chr4_2:5660284-5660303 Msa0585140:CDS 40.0%
! TAGTAGACGTTTGGAAGCAT+GGG + chr4_2:5660285-5660304 Msa0585140:CDS 40.0%
AAACCAAGTCCAACTCGAAA+TGG + chr4_2:5660342-5660361 Msa0585140:CDS 40.0%
! TTGTTGTTGCCATTTCGAGT+TGG - chr4_2:5660354-5660373 None:intergenic 40.0%
AGCATCTAGGAGTGAAGAAA+TGG + chr4_2:5660393-5660412 Msa0585140:CDS 40.0%
GAAATGGCAATTATGGGTCA+CGG + chr4_2:5660409-5660428 Msa0585140:CDS 40.0%
CATTAATAGGTACCCCAACA+TGG - chr4_2:5660435-5660454 None:intergenic 40.0%
!! ATCTCAGGTTGAGGCTCATA+AGG - chr4_2:5659986-5660005 None:intergenic 45.0%
ATGAGCCTCAACCTGAGATT+TGG + chr4_2:5659987-5660006 Msa0585140:CDS 45.0%
! AAAGGCCAAATCTCAGGTTG+AGG - chr4_2:5659995-5660014 None:intergenic 45.0%
TCAGGTAAAGGCCAAATCTC+AGG - chr4_2:5660001-5660020 None:intergenic 45.0%
! TGAGATTTGGCCTTTACCTG+AGG + chr4_2:5660000-5660019 Msa0585140:CDS 45.0%
! GAGATTTGGCCTTTACCTGA+GGG + chr4_2:5660001-5660020 Msa0585140:CDS 45.0%
! AGATTTGGCCTTTACCTGAG+GGG + chr4_2:5660002-5660021 Msa0585140:CDS 45.0%
!! TTGCCATTTCGAGTTGGACT+TGG - chr4_2:5660348-5660367 None:intergenic 45.0%
CTAGATGCTGCTAGAAGTGA+TGG - chr4_2:5660382-5660401 None:intergenic 45.0%
CATCACTTCTAGCAGCATCT+AGG + chr4_2:5660380-5660399 Msa0585140:CDS 45.0%
CCAGAATTGACCTCACGAAA+TGG - chr4_2:5660526-5660545 None:intergenic 45.0%
CCATTTCGTGAGGTCAATTC+TGG + chr4_2:5660523-5660542 Msa0585140:CDS 45.0%
!! GTGAGGTCAATTCTGGAGTT+TGG + chr4_2:5660530-5660549 Msa0585140:CDS 45.0%
ACAGGCTTCAATGCCACAGA+GGG - chr4_2:5659948-5659967 None:intergenic 50.0%
GAAGCCTGTGCCATAGTGTA+TGG + chr4_2:5659959-5659978 Msa0585140:CDS 50.0%
AGGTCCATACACTATGGCAC+AGG - chr4_2:5659966-5659985 None:intergenic 50.0%
! GATTTGGCCTTTACCTGAGG+GGG + chr4_2:5660003-5660022 Msa0585140:CDS 50.0%
CTTGACACAAAGGGTCCTGA+AGG + chr4_2:5660102-5660121 Msa0585140:CDS 50.0%
GATGCTGCTAGAAGTGATGG+TGG - chr4_2:5660379-5660398 None:intergenic 50.0%
ATTATGGGTCACGGCCATGT+TGG + chr4_2:5660418-5660437 Msa0585140:CDS 50.0%
TTATGGGTCACGGCCATGTT+GGG + chr4_2:5660419-5660438 Msa0585140:CDS 50.0%
!! TTGATGGACTCAATGGTGGC+TGG + chr4_2:5660481-5660500 Msa0585140:CDS 50.0%
!! AGAGACAGTGCCATTTCGTG+AGG + chr4_2:5660513-5660532 Msa0585140:CDS 50.0%
GCTGAACTTAGCACCCTCTG+TGG + chr4_2:5659932-5659951 Msa0585140:CDS 55.0%
CACAGGCTTCAATGCCACAG+AGG - chr4_2:5659949-5659968 None:intergenic 55.0%
GATTGGACCCCCTCAGGTAA+AGG - chr4_2:5660013-5660032 None:intergenic 55.0%
TATGGGTCACGGCCATGTTG+GGG + chr4_2:5660420-5660439 Msa0585140:CDS 55.0%
AGCACAGATTGGACCCCCTC+AGG - chr4_2:5660019-5660038 None:intergenic 60.0%
Chromosome Type Strat End Strand Name
chr4_2 gene 5659833 5660570 5659833 ID=Msa0585140;Name=Msa0585140
chr4_2 mRNA 5659833 5660570 5659833 ID=Msa0585140-mRNA-1;Parent=Msa0585140;Name=Msa0585140-mRNA-1;_AED=0.03;_eAED=0.03;_QI=0|-1|0|1|-1|1|1|0|245
chr4_2 exon 5659833 5660570 5659833 ID=Msa0585140-mRNA-1:exon:1353;Parent=Msa0585140-mRNA-1
chr4_2 CDS 5659833 5660570 5659833 ID=Msa0585140-mRNA-1:cds;Parent=Msa0585140-mRNA-1
Gene Sequence

>Msa0585140

ATGGGTAGAAGAAGTAAGGTTAAACTTGCCTTCATTGTCAATGATGTTGCAAGGAAAGCATCATACAAGAAAAGAACGAAGGGTCTATTGAAAAAGGTTGCTGAACTTAGCACCCTCTGTGGCATTGAAGCCTGTGCCATAGTGTATGGACCTTATGAGCCTCAACCTGAGATTTGGCCTTTACCTGAGGGGGTCCAATCTGTGCTCTCAAAATTCATGACGATGCACGAGTTTCAAAAGTGCAAGAAAATGATGAACCAAGAGACTTTCTTGACACAAAGGGTCCTGAAGGCTGAAGAGAAATTGAAGAAACAAAGAAAAGAAAATAGGGAGCAAGAGATGACAATACTCATGAGTCAATGTCTTAATGAAGGTAAAGTTGTGCATGACAATATGTCAACAATGGATATGAGTTATCTTGCTTGGTTGATTGACCACAATTTGAAGGATGTTAGTAGACGTTTGGAAGCATGGGATAACAATGATCAAAATCAAATCATGGCTATTCAAAACCAAGTCCAACTCGAAATGGCAACAACAATACCACCATCACTTCTAGCAGCATCTAGGAGTGAAGAAATGGCAATTATGGGTCACGGCCATGTTGGGGTACCTATTAATGATGATGACATTATGCAAAGTCAATTATTGATGGACTCAATGGTGGCTGGTAATGTGCAAGAGACAGTGCCATTTCGTGAGGTCAATTCTGGAGTTTGGTCTGATTTACTACCTTGA
Protein sequence

>Msa0585140

MGRRSKVKLAFIVNDVARKASYKKRTKGLLKKVAELSTLCGIEACAIVYGPYEPQPEIWPLPEGVQSVLSKFMTMHEFQKCKKMMNQETFLTQRVLKAEEKLKKQRKENREQEMTILMSQCLNEGKVVHDNMSTMDMSYLAWLIDHNLKDVSRRLEAWDNNDQNQIMAIQNQVQLEMATTIPPSLLAASRSEEMAIMGHGHVGVPINDDDIMQSQLLMDSMVAGNVQETVPFREVNSGVWSDLLP*