AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa ssp. caerulea / MsaG001944

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsaG001944 MtrunA17_Chr1g0169561 88.328 317 36 1 1 317 1 316 0.0 549
MsaG001944 MtrunA17_Chr1g0169521 87.382 317 39 1 1 317 1 316 0.0 539
MsaG001944 MtrunA17_Chr1g0174001 70.408 196 44 3 135 317 1 195 1.80e-89 265
MsaG001944 MtrunA17_Chr7g0214511 56.356 236 76 9 94 317 67 287 6.24e-65 206
MsaG001944 MtrunA17_Chr1g0172861 37.202 336 119 14 5 317 12 278 5.20e-39 139
MsaG001944 MtrunA17_Chr1g0174871 36.735 294 134 10 37 316 29 284 8.29e-38 135
MsaG001944 MtrunA17_Chr1g0172961 34.859 284 116 12 5 269 12 245 5.36e-29 112
MsaG001944 MtrunA17_Chr1g0193731 37.594 266 109 11 78 316 35 270 1.06e-27 109
MsaG001944 MtrunA17_Chr1g0174861 41.143 175 79 5 115 282 67 224 1.95e-26 104
MsaG001944 MtrunA17_Chr4g0037041 39.429 175 58 5 13 184 10 139 2.43e-24 97.8
MsaG001944 MtrunA17_Chr1g0180581 35.111 225 84 8 94 317 57 220 2.10e-20 87.8
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 62 sgRNAs with CRISPR-Local

Find sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TCGAAATTCCTGACAACTTT+TGG 0.230394 1:-28933577 None:intergenic
ACCGAAGATGAAACCGAATT+AGG 0.275613 1:+28933553 MsaT001944.1:CDS
AACAGAAAAGAAACACTAAT+TGG 0.288536 1:-28933638 None:intergenic
AGATTGAAGAAGAGTGTTAG+AGG 0.300936 1:-28932885 None:intergenic
CCCTAATTCGGTTTCATCTT+CGG 0.303612 1:-28933554 None:intergenic
CATTGTTATACATGTCTTAC+GGG 0.356166 1:+28933308 MsaT001944.1:CDS
ATTATCATCCACCGTATTGC+TGG 0.360275 1:-28933365 None:intergenic
GTACCCTTCTTCAAACCCTT+TGG 0.366898 1:-28933109 None:intergenic
TACTTTGACAAGTCAGTTGC+TGG 0.381007 1:-28933190 None:intergenic
CCGAAGATGAAACCGAATTA+GGG 0.394408 1:+28933554 MsaT001944.1:CDS
ACATTGTTATACATGTCTTA+CGG 0.407102 1:+28933307 MsaT001944.1:CDS
GTTATGAGGGATCAACTAAA+AGG 0.407447 1:+28933332 MsaT001944.1:CDS
TCATCCAACAACGCTTTGAA+TGG 0.417838 1:+28933067 MsaT001944.1:CDS
TGTTACAAACATCACATGTA+TGG 0.417941 1:-28933036 None:intergenic
CATAATCATGATCATGATGA+TGG 0.425720 1:+28933001 MsaT001944.1:CDS
AGCAGCAATATGCCTTCTCC+TGG 0.432642 1:-28933251 None:intergenic
AGTGTTAGAGGAGCGGTGAA+TGG 0.433506 1:-28932873 None:intergenic
GGCTCTGTTCCAAGGAAGAT+GGG 0.441032 1:-28933153 None:intergenic
ACCGACTGCCCCATCTTCCT+TGG 0.446430 1:+28933144 MsaT001944.1:CDS
TCTTCTTGCCTTCAATATCA+AGG 0.449412 1:-28933525 None:intergenic
TACTCCAAAGGGTTTGAAGA+AGG 0.451848 1:+28933105 MsaT001944.1:CDS
GTCTCTAACCTTGATATTGA+AGG 0.457506 1:+28933517 MsaT001944.1:CDS
AACTGTAGATTCTTGAACCT+GGG 0.459451 1:-28932796 None:intergenic
TGATCATGATGATGGGAAAC+CGG 0.467877 1:+28933009 MsaT001944.1:CDS
TCAAACATCACAAGATTCAA+AGG 0.476909 1:+28933486 MsaT001944.1:CDS
ATGTCCATTCAAAGCGTTGT+TGG 0.483248 1:-28933071 None:intergenic
TGGCTCTGTTCCAAGGAAGA+TGG 0.484956 1:-28933154 None:intergenic
AATTAGGGCCAAAAGTTGTC+AGG 0.486858 1:+28933569 MsaT001944.1:CDS
CAACTGTAGATTCTTGAACC+TGG 0.492609 1:-28932797 None:intergenic
ACATCACATGTATGGTTCTC+CGG 0.495209 1:-28933028 None:intergenic
TGTCACAAAACATTCACCTC+TGG 0.499496 1:+28932827 MsaT001944.1:CDS
ATGAGATTTCATACTCCAAA+GGG 0.500060 1:+28933094 MsaT001944.1:CDS
CGTTATTCACAGCATGATCA+TGG 0.509884 1:-28932925 None:intergenic
TATCATCTTCAAGAGTCTGT+TGG 0.516591 1:-28932766 None:intergenic
CATGATCATGCTGTGAATAA+CGG 0.518528 1:+28932926 MsaT001944.1:CDS
TTGCCACAACGAAAAGAACT+TGG 0.525913 1:+28933429 MsaT001944.1:CDS
ATATCAAGGTTAGAGACTGC+AGG 0.538103 1:-28933511 None:intergenic
CTCAAGATGGCTCTGTTCCA+AGG 0.539755 1:-28933161 None:intergenic
ACTCCAAAGGGTTTGAAGAA+GGG 0.545861 1:+28933106 MsaT001944.1:CDS
GCAGAAGATTTCCAGCAATA+CGG 0.546299 1:+28933354 MsaT001944.1:CDS
TCAAACGAATGGTGAGAAGA+AGG 0.549246 1:-28932713 None:intergenic
ACCTCTGGTAAATCACTTGG+TGG 0.556710 1:+28932842 MsaT001944.1:CDS
AACAAGGTGTGATGCTAACA+AGG 0.557593 1:+28933401 MsaT001944.1:CDS
GAAGAAGAGTGTTAGAGGAG+CGG 0.560783 1:-28932880 None:intergenic
TCATCTTCAAAATCATCACT+TGG 0.561665 1:-28933613 None:intergenic
TTCACCTCTGGTAAATCACT+TGG 0.575760 1:+28932839 MsaT001944.1:CDS
GGATGATAATGAGAAGATGA+AGG 0.579672 1:+28933378 MsaT001944.1:CDS
ATAATCATGATCATGATGAT+GGG 0.591510 1:+28933002 MsaT001944.1:CDS
TATGAGATTTCATACTCCAA+AGG 0.603569 1:+28933093 MsaT001944.1:CDS
AATGAGAAGATGAAGGAACA+AGG 0.607433 1:+28933385 MsaT001944.1:CDS
TCCAAGGAAGATGGGGCAGT+CGG 0.610571 1:-28933145 None:intergenic
GCAGCAATATGCCTTCTCCT+GGG 0.615845 1:-28933250 None:intergenic
TCTGTTGGTGATAATGATCA+TGG 0.616583 1:-28932751 None:intergenic
TTGCTGGTCGAAACTCAAGA+TGG 0.617863 1:-28933174 None:intergenic
ACGAAAAGAACTTGGTGCTG+AGG 0.634219 1:+28933437 MsaT001944.1:CDS
TATTGCTGCTGATGATGATG+AGG 0.663094 1:+28933264 MsaT001944.1:CDS
GAAGATTTCCAGCAATACGG+TGG 0.664760 1:+28933357 MsaT001944.1:CDS
GCTCTGTTCCAAGGAAGATG+GGG 0.667093 1:-28933152 None:intergenic
ATTGTTATACATGTCTTACG+GGG 0.683485 1:+28933309 MsaT001944.1:CDS
TTGTTATACATGTCTTACGG+GGG 0.692006 1:+28933310 MsaT001944.1:CDS
ACCACCAAGTGATTTACCAG+AGG 0.717389 1:-28932843 None:intergenic
GATCATGCTGTGAATAACGG+CGG 0.741138 1:+28932929 MsaT001944.1:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
Chromosome Type Strat End Strand Name
Chr1 gene 28932692 28933645 28932692 ID=MsaG001944
Chr1 mRNA 28932692 28933645 28932692 ID=MsaT001944.1;Parent=MsaG001944
Chr1 exon 28932692 28933645 28932692 ID=MsaT001944.1.exon1;Parent=MsaT001944.1
Chr1 CDS 28932692 28933645 28932692 ID=cds.MsaT001944.1;Parent=MsaT001944.1
Gene Sequence

>MsaT001944.1

ATGAACAAACACTATTCTTCACCTTCTTCTCACCATTCGTTTGATAAACCCAAAAACAGCCATGATCATTATCACCAACAGACTCTTGAAGATGATAAGAAAAACCCAGGTTCAAGAATCTACAGTTGTGAGTTTTGTCACAAAACATTCACCTCTGGTAAATCACTTGGTGGTCACAAAACCATTCACCGCTCCTCTAACACTCTTCTTCAATCTAAAACAAACAAACAGATCCATGATCATGCTGTGAATAACGGCGGCACCTTGAAGAAGACTACAAAAATTACTTGGGTTTTTTCTTCTTCTCTTCATAATCATGATCATGATGATGGGAAACCGGAGAACCATACATGTGATGTTTGTAACAAAGTTTTTTCATCCAACAACGCTTTGAATGGACATATGAGATTTCATACTCCAAAGGGTTTGAAGAAGGGTACTATTATTCACTCACCGACTGCCCCATCTTCCTTGGAACAGAGCCATCTTGAGTTTCGACCAGCAACTGACTTGTCAAAGTACTTGCCACCAATATCGTATAAAACCAAAAAACGGAGTCCCAGGAGAAGGCATATTGCTGCTGATGATGATGAGGAAATTACTCTTGCTGCAAAAACATTGTTATACATGTCTTACGGGGGTTATGAGGGATCAACTAAAAGGCAGAAGATTTCCAGCAATACGGTGGATGATAATGAGAAGATGAAGGAACAAGGTGTGATGCTAACAAGGTGTGTTTGCCACAACGAAAAGAACTTGGTGCTGAGGTTGAAGATTCCAAAAGATGTGATTTTTCAAACATCACAAGATTCAAAGGAACCTGCAGTCTCTAACCTTGATATTGAAGGCAAGAAGAATGTTACCGAAGATGAAACCGAATTAGGGCCAAAAGTTGTCAGGAATTTCGATTTGAATGAGCTTCCAAGTGATGATTTTGAAGATGAAACCAATTAG
Protein sequence

>MsaT001944.1

MNKHYSSPSSHHSFDKPKNSHDHYHQQTLEDDKKNPGSRIYSCEFCHKTFTSGKSLGGHKTIHRSSNTLLQSKTNKQIHDHAVNNGGTLKKTTKITWVFSSSLHNHDHDDGKPENHTCDVCNKVFSSNNALNGHMRFHTPKGLKKGTIIHSPTAPSSLEQSHLEFRPATDLSKYLPPISYKTKKRSPRRRHIAADDDEEITLAAKTLLYMSYGGYEGSTKRQKISSNTVDDNEKMKEQGVMLTRCVCHNEKNLVLRLKIPKDVIFQTSQDSKEPAVSNLDIEGKKNVTEDETELGPKVVRNFDLNELPSDDFEDETN*