AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1205800

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1205800 MtrunA17_Chr4g0055041 96.739 184 5 1 18 200 173 356 3.52e-123 353
Msa1205800 MtrunA17_Chr2g0283381 66.667 183 61 0 18 200 176 358 1.83e-83 252
Msa1205800 MtrunA17_Chr7g0249781 59.563 183 74 0 18 200 160 342 2.21e-69 215
Msa1205800 MtrunA17_Chr3g0102091 51.500 200 92 2 3 200 169 365 3.44e-64 203
Msa1205800 MtrunA17_Chr6g0483671 50.336 149 74 0 52 200 3 151 8.35e-51 162
Msa1205800 MtrunA17_Chr5g0426921 34.595 185 120 1 18 201 159 343 1.16e-32 120
Msa1205800 MtrunA17_Chr3g0132551 29.891 184 129 0 18 201 162 345 6.58e-29 110
Msa1205800 MtrunA17_Chr8g0346091 29.282 181 128 0 18 198 180 360 5.53e-25 100
Msa1205800 MtrunA17_Chr2g0296491 30.899 178 119 2 19 195 202 376 5.18e-20 86.7
Msa1205800 MtrunA17_Chr2g0296481 28.571 168 116 2 32 198 196 360 1.70e-18 82.4
Msa1205800 MtrunA17_Chr3g0132561 34.259 108 71 0 94 201 203 310 3.65e-17 78.2
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1205800 AT4G18220.1 59.563 183 74 0 18 200 176 358 1.72e-70 219
Msa1205800 AT4G18210.1 58.470 183 76 0 18 200 176 358 2.22e-67 211
Msa1205800 AT1G44750.7 53.552 183 85 0 18 200 98 280 7.45e-63 197
Msa1205800 AT1G44750.5 53.552 183 85 0 18 200 98 280 7.45e-63 197
Msa1205800 AT1G44750.4 53.552 183 85 0 18 200 98 280 7.45e-63 197
Msa1205800 AT1G44750.8 53.552 183 85 0 18 200 98 280 7.45e-63 197
Msa1205800 AT1G44750.3 53.552 183 85 0 18 200 98 280 7.45e-63 197
Msa1205800 AT1G44750.6 53.552 183 85 0 18 200 162 344 2.46e-61 195
Msa1205800 AT1G44750.2 53.552 183 85 0 18 200 162 344 2.46e-61 195
Msa1205800 AT1G44750.1 53.552 183 85 0 18 200 174 356 2.76e-61 195
Msa1205800 AT4G18205.1 53.005 183 86 0 18 200 173 355 3.78e-57 185
Msa1205800 AT4G18197.1 48.824 170 87 0 31 200 189 358 6.70e-55 179
Msa1205800 AT4G18195.1 53.552 183 85 0 18 200 179 361 9.91e-53 174
Msa1205800 AT4G08700.1 47.283 184 97 0 17 200 162 345 8.77e-52 170
Msa1205800 AT4G18190.1 50.267 187 89 1 18 200 169 355 7.90e-48 161
Msa1205800 AT5G41160.1 45.652 184 100 0 17 200 165 348 4.86e-47 158
Msa1205800 AT2G33750.2 36.413 184 117 0 18 201 141 324 9.26e-37 131
Msa1205800 AT1G28220.1 30.978 184 127 0 18 201 139 322 7.02e-34 124
Msa1205800 AT2G33750.1 34.359 195 117 1 18 201 141 335 1.88e-33 122
Msa1205800 AT1G28230.1 32.609 184 123 1 18 200 145 328 4.32e-30 114
Msa1205800 AT1G57980.1 37.179 156 88 2 53 198 217 372 4.03e-24 98.2
Msa1205800 AT1G47603.1 35.610 205 117 5 6 198 172 373 5.87e-24 97.8
Msa1205800 AT1G57990.1 35.897 156 90 2 53 198 213 368 2.24e-22 93.6
Msa1205800 AT1G57943.1 33.146 178 105 4 35 198 199 376 2.96e-21 90.5
Msa1205800 AT1G57943.2 33.146 178 105 4 35 198 198 375 3.25e-21 90.5
Msa1205800 AT1G19770.1 31.746 189 111 3 22 199 203 384 5.66e-20 87.0
Msa1205800 AT2G24220.1 27.841 176 127 0 18 193 165 340 7.66e-20 86.3
Msa1205800 AT2G24220.2 27.841 176 127 0 18 193 183 358 8.54e-20 86.3
Msa1205800 AT1G75470.1 34.194 155 91 2 55 198 218 372 1.81e-19 85.5
Msa1205800 AT1G09860.1 39.865 148 79 3 35 175 190 334 3.36e-17 79.0
Msa1205800 AT1G30840.2 28.402 169 116 2 32 198 171 336 1.66e-14 71.2
Msa1205800 AT1G30840.1 28.402 169 116 2 32 198 171 336 1.66e-14 71.2

Find 43 sgRNAs with CRISPR-Local

Find 48 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TAGCCTTAATGTTAGCAATA+TGG 0.213802 8_1:-62284026 Msa1205800:CDS
GCTACTTGTGCTTGTGTTGC+TGG 0.238139 8_1:-62284297 Msa1205800:CDS
CCAAGTACTCGCTTATCTTT+AGG 0.253149 8_1:+62284453 None:intergenic
TTATTGTTCTCAAATGTAAT+AGG 0.278188 8_1:-62284123 Msa1205800:CDS
CATATATAATGACTTTGTTT+TGG 0.282504 8_1:-62284206 Msa1205800:CDS
GTATCTTCCATTGGTATGTT+AGG 0.292638 8_1:-62284165 Msa1205800:CDS
AGCCTTAATGTTAGCAATAT+GGG 0.317391 8_1:-62284025 Msa1205800:CDS
ATATGAATGCTGTGAACTTT+TGG 0.321106 8_1:+62284548 None:intergenic
TCCCCATATTGCTAACATTA+AGG 0.322350 8_1:+62284023 None:intergenic
GGAGATGAAGGAATATGAAC+TGG 0.366582 8_1:-62284238 Msa1205800:CDS
CCTAAAGATAAGCGAGTACT+TGG 0.390852 8_1:-62284453 Msa1205800:CDS
AGAATGGAAAAGTTTGAATA+AGG 0.399319 8_1:-62284259 Msa1205800:CDS
GCACAAGTAGCGACGAAAGA+AGG 0.407661 8_1:+62284309 None:intergenic
GTCCTCAGAATCGTTATTGA+TGG 0.418883 8_1:+62284488 None:intergenic
TCAGAGATGTTGATAAATAT+AGG 0.424768 8_1:+62283993 None:intergenic
CTACTTGTGCTTGTGTTGCT+GGG 0.432451 8_1:-62284296 Msa1205800:CDS
CTTGGATTCGTCTTCACCCT+TGG 0.444186 8_1:-62284435 Msa1205800:CDS
TCTTCCATGACAAAATCAAC+GGG 0.471038 8_1:-62284059 Msa1205800:CDS
GAAGAAAATAACAGCAAGGA+TGG 0.477070 8_1:+62284077 None:intergenic
GGTTGTTTGCAAGTGGAGAA+TGG 0.482806 8_1:-62284275 Msa1205800:CDS
CATGTCCAAGATAACAGAAA+AGG 0.503363 8_1:+62284341 None:intergenic
ATCGTTATTGATGGCAAGTA+GGG 0.507986 8_1:+62284497 None:intergenic
AAGTTTGAATAAGGAGATGA+AGG 0.509849 8_1:-62284250 Msa1205800:CDS
ACAGCAAGGATGGGACCTAC+AGG 0.527733 8_1:+62284087 None:intergenic
TTCTTCCATGACAAAATCAA+CGG 0.528604 8_1:-62284060 Msa1205800:CDS
CACAAGTAGCGACGAAAGAA+GGG 0.536717 8_1:+62284310 None:intergenic
AATCGTTATTGATGGCAAGT+AGG 0.540072 8_1:+62284496 None:intergenic
AACTAATCCTAACATACCAA+TGG 0.561168 8_1:+62284158 None:intergenic
ACATGGCAAGTATCTTCCAT+TGG 0.573996 8_1:-62284174 Msa1205800:CDS
TGTCAAAAGAAAGCTGCACA+AGG 0.574825 8_1:+62284382 None:intergenic
GTTGCTGGGTTGTTTGCAAG+TGG 0.582152 8_1:-62284282 Msa1205800:CDS
TGCCATCAATAACGATTCTG+AGG 0.582388 8_1:-62284490 Msa1205800:CDS
GAAGGAATATGAACTGGGAA+AGG 0.585101 8_1:-62284232 Msa1205800:CDS
GCCTTAATGTTAGCAATATG+GGG 0.590818 8_1:-62284024 Msa1205800:CDS
GAGATGAAGGAATATGAACT+GGG 0.604093 8_1:-62284237 Msa1205800:CDS
AAATGTAACAGATGCACCAA+GGG 0.607913 8_1:+62284419 None:intergenic
AAGAAAATAACAGCAAGGAT+GGG 0.616093 8_1:+62284078 None:intergenic
CATGGAAGAAAATAACAGCA+AGG 0.631020 8_1:+62284073 None:intergenic
CTCAAATGTAATAGGTACAG+TGG 0.634079 8_1:-62284115 Msa1205800:CDS
GGTACAGTGGTACTTCCTGT+AGG 0.644346 8_1:-62284102 Msa1205800:CDS
AAAATGTAACAGATGCACCA+AGG 0.653920 8_1:+62284418 None:intergenic
GTCAAAAGAAAGCTGCACAA+GGG 0.669271 8_1:+62284383 None:intergenic
CTTCCATGACAAAATCAACG+GGG 0.691412 8_1:-62284058 Msa1205800:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! CATATATAATGACTTTGTTT+TGG - chr8_1:62284363-62284382 Msa1205800:CDS 20.0%
!! TTATTGTTCTCAAATGTAAT+AGG - chr8_1:62284446-62284465 Msa1205800:CDS 20.0%
! AGAATGGAAAAGTTTGAATA+AGG - chr8_1:62284310-62284329 Msa1205800:CDS 25.0%
!! TCAGAGATGTTGATAAATAT+AGG + chr8_1:62284579-62284598 None:intergenic 25.0%
! TATGAATGCTGTGAACTTTT+GGG + chr8_1:62284023-62284042 None:intergenic 30.0%
! ATATGAATGCTGTGAACTTT+TGG + chr8_1:62284024-62284043 None:intergenic 30.0%
! TGAAACCTTTTCTGTTATCT+TGG - chr8_1:62284223-62284242 Msa1205800:CDS 30.0%
AAGTTTGAATAAGGAGATGA+AGG - chr8_1:62284319-62284338 Msa1205800:CDS 30.0%
AACTAATCCTAACATACCAA+TGG + chr8_1:62284414-62284433 None:intergenic 30.0%
AAGAAAATAACAGCAAGGAT+GGG + chr8_1:62284494-62284513 None:intergenic 30.0%
TTCTTCCATGACAAAATCAA+CGG - chr8_1:62284509-62284528 Msa1205800:CDS 30.0%
! TAGCCTTAATGTTAGCAATA+TGG - chr8_1:62284543-62284562 Msa1205800:CDS 30.0%
AGCCTTAATGTTAGCAATAT+GGG - chr8_1:62284544-62284563 Msa1205800:CDS 30.0%
! ATCGTTATTGATGGCAAGTA+GGG + chr8_1:62284075-62284094 None:intergenic 35.0%
! AATCGTTATTGATGGCAAGT+AGG + chr8_1:62284076-62284095 None:intergenic 35.0%
AAATGTAACAGATGCACCAA+GGG + chr8_1:62284153-62284172 None:intergenic 35.0%
AAAATGTAACAGATGCACCA+AGG + chr8_1:62284154-62284173 None:intergenic 35.0%
CATGTCCAAGATAACAGAAA+AGG + chr8_1:62284231-62284250 None:intergenic 35.0%
GAGATGAAGGAATATGAACT+GGG - chr8_1:62284332-62284351 Msa1205800:CDS 35.0%
GTATCTTCCATTGGTATGTT+AGG - chr8_1:62284404-62284423 Msa1205800:CDS 35.0%
CTCAAATGTAATAGGTACAG+TGG - chr8_1:62284454-62284473 Msa1205800:CDS 35.0%
GAAGAAAATAACAGCAAGGA+TGG + chr8_1:62284495-62284514 None:intergenic 35.0%
CATGGAAGAAAATAACAGCA+AGG + chr8_1:62284499-62284518 None:intergenic 35.0%
TCTTCCATGACAAAATCAAC+GGG - chr8_1:62284510-62284529 Msa1205800:CDS 35.0%
GCCTTAATGTTAGCAATATG+GGG - chr8_1:62284545-62284564 Msa1205800:CDS 35.0%
TCCCCATATTGCTAACATTA+AGG + chr8_1:62284549-62284568 None:intergenic 35.0%
!! CTGTGAACTTTTGGGAGTTA+AGG + chr8_1:62284015-62284034 None:intergenic 40.0%
TGCCATCAATAACGATTCTG+AGG - chr8_1:62284079-62284098 Msa1205800:CDS 40.0%
GTCCTCAGAATCGTTATTGA+TGG + chr8_1:62284084-62284103 None:intergenic 40.0%
CCAAGTACTCGCTTATCTTT+AGG + chr8_1:62284119-62284138 None:intergenic 40.0%
CCTAAAGATAAGCGAGTACT+TGG - chr8_1:62284116-62284135 Msa1205800:CDS 40.0%
GTCAAAAGAAAGCTGCACAA+GGG + chr8_1:62284189-62284208 None:intergenic 40.0%
TGTCAAAAGAAAGCTGCACA+AGG + chr8_1:62284190-62284209 None:intergenic 40.0%
GGAGATGAAGGAATATGAAC+TGG - chr8_1:62284331-62284350 Msa1205800:CDS 40.0%
GAAGGAATATGAACTGGGAA+AGG - chr8_1:62284337-62284356 Msa1205800:CDS 40.0%
!! TGTTTTGGATTGCTGTGACA+TGG - chr8_1:62284378-62284397 Msa1205800:CDS 40.0%
ACATGGCAAGTATCTTCCAT+TGG - chr8_1:62284395-62284414 Msa1205800:CDS 40.0%
CTTCCATGACAAAATCAACG+GGG - chr8_1:62284511-62284530 Msa1205800:CDS 40.0%
CACAAGTAGCGACGAAAGAA+GGG + chr8_1:62284262-62284281 None:intergenic 45.0%
! CTACTTGTGCTTGTGTTGCT+GGG - chr8_1:62284273-62284292 Msa1205800:CDS 45.0%
GGTTGTTTGCAAGTGGAGAA+TGG - chr8_1:62284294-62284313 Msa1205800:CDS 45.0%
!!! TCACCCCGTTGATTTTGTCA+TGG + chr8_1:62284517-62284536 None:intergenic 45.0%
CTTGGATTCGTCTTCACCCT+TGG - chr8_1:62284134-62284153 Msa1205800:CDS 50.0%
GCACAAGTAGCGACGAAAGA+AGG + chr8_1:62284263-62284282 None:intergenic 50.0%
GCTACTTGTGCTTGTGTTGC+TGG - chr8_1:62284272-62284291 Msa1205800:CDS 50.0%
GTTGCTGGGTTGTTTGCAAG+TGG - chr8_1:62284287-62284306 Msa1205800:CDS 50.0%
GGTACAGTGGTACTTCCTGT+AGG - chr8_1:62284467-62284486 Msa1205800:CDS 50.0%
ACAGCAAGGATGGGACCTAC+AGG + chr8_1:62284485-62284504 None:intergenic 55.0%
Chromosome Type Strat End Strand Name
chr8_1 gene 62283993 62284598 62283993 ID=Msa1205800;Name=Msa1205800
chr8_1 mRNA 62283993 62284598 62283993 ID=Msa1205800-mRNA-1;Parent=Msa1205800;Name=Msa1205800-mRNA-1;_AED=0.29;_eAED=0.34;_QI=0|-1|0|1|-1|1|1|0|201
chr8_1 exon 62283993 62284598 62283993 ID=Msa1205800-mRNA-1:exon:20223;Parent=Msa1205800-mRNA-1
chr8_1 CDS 62283993 62284598 62283993 ID=Msa1205800-mRNA-1:cds;Parent=Msa1205800-mRNA-1
Gene Sequence

>Msa1205800

ATGCAGTATTTTCTTACTTCCTTAACTCCCAAAAGTTCACAGCATTCATATTCAATTCTTCTGCTTACTATTTCGTCTGCCCTACTTGCCATCAATAACGATTCTGAGGACTCGACGAATCTTCCTAAAGATAAGCGAGTACTTGGATTCGTCTTCACCCTTGGTGCATCTGTTACATTTTCTTTATATCTCTCCCTTGTGCAGCTTTCTTTTGACAAAGTTATAAAAAGTGAAACCTTTTCTGTTATCTTGGACATGCAGTTTTACCCTTCTTTCGTCGCTACTTGTGCTTGTGTTGCTGGGTTGTTTGCAAGTGGAGAATGGAAAAGTTTGAATAAGGAGATGAAGGAATATGAACTGGGAAAGGTGTCATATATAATGACTTTGTTTTGGATTGCTGTGACATGGCAAGTATCTTCCATTGGTATGTTAGGATTAGTTTTAGATGTATCTTTATTGTTCTCAAATGTAATAGGTACAGTGGTACTTCCTGTAGGTCCCATCCTTGCTGTTATTTTCTTCCATGACAAAATCAACGGGGTGAAGTTTATAGCCTTAATGTTAGCAATATGGGGATTTCTTTCCTATATTTATCAACATCTCTGA
Protein sequence

>Msa1205800

MQYFLTSLTPKSSQHSYSILLLTISSALLAINNDSEDSTNLPKDKRVLGFVFTLGASVTFSLYLSLVQLSFDKVIKSETFSVILDMQFYPSFVATCACVAGLFASGEWKSLNKEMKEYELGKVSYIMTLFWIAVTWQVSSIGMLGLVLDVSLLFSNVIGTVVLPVGPILAVIFFHDKINGVKFIALMLAIWGFLSYIYQHL*