Origin IGS: gacaaaaagaagctcagtgcgagagggggatttcctctttacactgagttttttgtttggagtttttagtttaaaatctttattcagtttaaaattatttccaaatagaacaaaattcttgacagatgtaattctagatgttacaattaaggaaaatcgattcgatatagaaataaattggagggagt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 actccctccaatttatttctatatcgaatcgattttccttaattgtaacatctagaattacatctgtcaagaattttgttctatttggaaataattttaaactgaataaagattttaaactaaaaactccaaacaaaaaactcagtgtaaagaggaaatccccctctcgcactgagcttctttttgtc Mask Tandem Repeat Region ================================================ gacaaaaagaagctcagtgcgagagggggatttcctctttacactgagttttttgtttggagtttttagtttaaaatctttattcagtttaaaattatttccaaatagaacaaaattcttgacagatgtaattctagatgttacaattaaggaaaatcgattcgatatagaaataaattggagggagt Find is-nt database================================================ Query_seq: SSA_0983:SSA_0984|SSA_0983:SSA_0984:Conserved uncharacterized protein:SlyA-like protein, putative:->->:987006..987193 188 gacaaaaagaagctcagtgcgagagggggatttcctctttacactgagttttttgtttggagtttttagtttaaaatctttattcagtttaaaattatttccaaatagaacaaaattcttgacagatgtaattctagatgttacaattaaggaaaatcgattcgatatagaaataaattggagggagt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0983:SSA_0984|SSA_0983:SSA_0984:Conserved uncharacterized protein:SlyA-like protein, putative:->->:987006..987193 188 gacaaaaagaagctcagtgcgagagggggatttcctctttacactgagttttttgtttggagtttttagtttaaaatctttattcagtttaaaattatttccaaatagaacaaaattcttgacagatgtaattctagatgttacaattaaggaaaatcgattcgatatagaaataaattggagggagt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0983:SSA_0984|SSA_0983:SSA_0984:Conserved uncharacterized protein:SlyA-like protein, putative:->->:987006..987193 188 gacaaaaagaagctcagtgcgagagggggatttcctctttacactgagttttttgtttggagtttttagtttaaaatctttattcagtttaaaattatttccaaatagaacaaaattcttgacagatgtaattctagatgttacaattaaggaaaatcgattcgatatagaaataaattggagggagt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gacaaaaagaagctcagtgcgagagggggatttcctctttacactgagttttttgtttggagtttttagtttaaaatctttattcagtttaaaattatttccaaatagaacaaaattcttgacagatgtaattctagatgttacaattaaggaaaatcgattcgatatagaaataaattggagggagt Predict ORF larger than 30AA ================================================ Protein_Len: 57 Strand: + Start: 17 End: 187 ................ M R E G D F L F T L S F L F G V F S L K S L F S L K L F P N R T K F L T D V I L D V T I K E N R F D I E I N W R E . Protein_Len: 58 Strand: - Start: 1 End: 174 V F L L E T R S P S K R K V S L K K N P T K L K F D K N L K F N N G F L V F N K V S T I R S T V I L S F R N S I S M .............. gacaaaaagaagctcagtgcgagagggggatttcctctttacactgagttttttgtttggagtttttagtttaaaatctttattcagtttaaaattatttccaaatagaacaaaattcttgacagatgtaattctagatgttacaattaaggaaaatcgattcgatatagaaataaattggagggagt Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ PromScan Matrix: RpoD-17 Strand: + Score: 90 Start: 118 End: 147 .....................................................................................................................CTTGACAGATGTAATTCTAGATGTTACAAT......................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ gacaaaaagaagctcagtgcgagagggggatttcctctttacactgagttttttgtttggagtttttagtttaaaatctttattcagtttaaaattatttccaaatagaacaaaattcttgacagatgtaattctagatgttacaattaaggaaaatcgattcgatatagaaataaattggagggagt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_0983:SSA_0984|SSA_0983:SSA_0984:Conserved uncharacterized protein:SlyA-like protein, putative:->->:987006..987193 188 gacaaaaagaagctcagtgcgagagggggatttcctctttacactgagttttttgtttggagtttttagtttaaaatctttattcagtttaaaattatttccaaatagaacaaaattcttgacagatgtaattctagatgttacaattaaggaaaatcgattcgatatagaaataaattggagggagt Intra-Species Hit: Count: 1 Min: 1 Max: 188 Len: 188 Subject: NC_009009_SSA_0983_SSA_0984|Conserved uncharacterized protein:SlyA-like protein, putative|POSITIVE:POSITIVE|[987006,987193]|188 HSP 1 e-value: 7.0E-43 bit: 174.0 Len: 88 Query Start:101 Query End:188 Subject Strand: POSITIVE Subject Start: 101 Subject End: 188 ....................................................................................................ccaaatagaacaaaattcttgacagatgtaattctagatgttacaattaaggaaaatcgattcgatatagaaataaattggagggagt ....................................................................................................ccaaatagaacaaaattcttgacagatgtaattctagatgttacaattaaggaaaatcgattcgatatagaaataaattggagggagt HSP 2 e-value: 8.0E-18 bit: 91.7 Len: 46 Query Start:1 Query End:46 Subject Strand: POSITIVE Subject Start: 1 Subject End: 46 gacaaaaagaagctcagtgcgagagggggatttcctctttacactg.............................................................................................................................................. gacaaaaagaagctcagtgcgagagggggatttcctctttacactg.............................................................................................................................................. Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GACAAAAAGAAGCUCAGUGCGAGAGGGGGAUUUCCUCUUUACACUGAGUUUUUUGUUUGGAGUUUUUAGUUUAAAAUCUUUAUUCAGUUUAAAAUUAUUUCCAAAUAGAACAAAAUUCUUGACAGAUGUAAUUCUAGAUGUUACAAUUAAGGAAAAUCGAUUCGAUAUAGAAAUAAAUUGGAGGGAGU .........((((((((((..(((((((.....))))))).))))))))))(((((((((((....((((((.((((.........)))).)))))).)))))))))))......(((((((....((((((.......)))))).)))))))...((..((((((.((....)).))))))..)).. (-45.90) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACUCCCUCCAAUUUAUUUCUAUAUCGAAUCGAUUUUCCUUAAUUGUAACAUCUAGAAUUACAUCUGUCAAGAAUUUUGUUCUAUUUGGAAAUAAUUUUAAACUGAAUAAAGAUUUUAAACUAAAAACUCCAAACAAAAAACUCAGUGUAAAGAGGAAAUCCCCCUCUCGCACUGAGCUUCUUUUUGUC ............(((((((((.((.(((.(((..(((..((..(((((.........)))))..))....)))..)))))).)).)))))))))......................................(((((((.((((((((..(((((.......))))).))))))))....))))))). (-34.20) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 297 59 12 199 153 NC_009009:SSA_1476|5end_Phosphoglycerol_transferase,_alkaline_phosphatase_superfamily,_putative_1480173..1480403_POSITIVE 289 60 12 109 56 NC_009009:SSA_1863|5end_NH(3)-dependent_NAD(+)_synthetase,_putative_1859413..1859643_NEGATIVE 287 54 13 140 102 NC_009009:SSA_0163|5end_hypothetical_protein_162127..162357_POSITIVE 277 65 21 208 160 NC_009009:SSA_0363|5end_D-alanine/glycine/Na_permease,_putative_353858..354088_POSITIVE 276 54 11 201 156 NC_009009:SSA_1006|5end_Dextransucrase,_putative_1007076..1007306_POSITIVE 272 39 3 70 34 NC_009009:SSA_0796|5end_ABC-NBD_transporters_with_duplicated_ATPase_domains,_putative_777085..777315_POSITIVE 267 51 12 125 84 NC_009009:SSA_1676|5end_Transcriptional_regulator,_LytTr_family,_putative_1671313..1671543_NEGATIVE 262 59 12 194 131 NC_009009:SSA_1304|5end_hypothetical_protein_1323449..1323679_NEGATIVE 261 59 13 72 26 NC_009009:SSA_0374|5end_Peptide_methionine_sulfoxide_reductase_msrA/msrB,_putative_363163..363393_POSITIVE 259 52 13 42 2 NC_009009:SSA_0511|5end_Propanediol_utilization_kinase,_putative_509610..509840_POSITIVE 255 44 6 100 52 NC_009009:SSA_0294|5end_hypothetical_protein_287876..288106_NEGATIVE 252 46 5 119 78 NC_009009:SSA_0432|5end_Formate--tetrahydrofolate_ligase,_putative_434991..435221_NEGATIVE 249 51 14 140 88 NC_009009:SSA_1550|5end_hypothetical_protein_1552665..1552895_NEGATIVE 249 69 23 180 124 NC_009009:SSA_1299|5end_Maltose/maltodextrin_ABC_transport_system,_putative_1316629..1316859_POSITIVE 245 80 31 152 98 NC_009009:SSA_2278|5end_Ukp_protein,_putative_2281669..2281899_NEGATIVE 245 59 11 68 22 NC_009009:SSA_0838|5end_GtfB,_putative_825406..825636_POSITIVE 244 38 7 65 32 NC_009009:SSA_1948|5end_Oligopeptide-binding_lipoprotein_precursor,_putative_1942170..1942400_NEGATIVE 243 48 11 229 186 NC_009009:SSA_0538|5end_PduH_protein,_putative_533794..534024_POSITIVE 237 47 11 45 13 NC_009009:SSA_1783|5end_Xanthosine_triphosphate_pyrophosphatase_(NTPase/HAM1_family),_putative_1769106..1769336_NEGATIVE 236 35 8 41 11 NC_009009:SSA_0286|5end_Transaldolase-like_protein,_putative_278814..279044_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 470 50 3 80 32 NC_009009:SSA_0983|3end_Conserved_uncharacterized_protein_986945..987095_POSITIVE 297 60 12 135 64 NC_009009:SSA_1318|3end_GTP-binding_protein_lepA,_putative_1333989..1334139_NEGATIVE 294 28 5 55 28 NC_009009:SSA_0429|3end_Histidine_ammonia-lyase,_putative_429701..429851_NEGATIVE 289 60 12 112 59 NC_009009:SSA_1864|3end_Nicotinate_phosphoribosyltransferase_(NAPRTase),_subgroup_A,_putative_1859410..1859560_NEGATIVE 287 54 13 72 34 NC_009009:SSA_0162|3end_hypothetical_protein_162139..162289_POSITIVE 283 50 10 116 64 NC_009009:SSA_2296|3end_Transcriptional_regulator,_XRE_family,_putative_2298549..2298699_NEGATIVE 276 52 13 49 3 NC_009009:SSA_0510|3end_L-threonine-O-3-phosphate_decarboxylase,_putative_509697..509847_POSITIVE 267 51 12 102 61 NC_009009:SSA_1678|3end_ABC-type_multidrug_transport_system,_permease_component,_putative_1671336..1671486_NEGATIVE 263 69 21 108 62 NC_009009:SSA_1625|3end_Lactoylglutathione_lyase,_putative_1626577..1626727_NEGATIVE 262 59 12 118 55 NC_009009:SSA_1305|3end_hypothetical_protein_1323525..1323675_NEGATIVE 252 46 5 82 41 NC_009009:SSA_0433|3end_Methenyl_tetrahydrofolate_cyclohydrolase,_putative_435028..435178_NEGATIVE 250 70 21 101 55 NC_009009:SSA_0887|3end_hypothetical_protein_881165..881315_NEGATIVE 250 51 12 127 82 NC_009009:SSA_0214|3end_Single-strand_DNA-binding_protein_(conjugal_DNA-protein_transfer_system),_putative_210690..210840_POSITIVE 249 69 23 98 42 NC_009009:SSA_1298|3end_Maltose/maltodextrin_ABC_transporter,_sugar-binding_protein_MalX,_putative_1316627..1316777_POSITIVE 248 58 13 64 17 NC_009009:SSA_0172|3end_Transcriptional_regulator,_XRE_family,_putative_169672..169822_POSITIVE 247 60 15 98 41 NC_009009:SSA_2108|3end_Glyceraldehyde_3-phosphate_dehydrogenase,_putative_2111457..2111607_NEGATIVE 245 80 31 150 96 NC_009009:SSA_2279|3end_hypothetical_protein_2281671..2281821_NEGATIVE 245 59 11 125 67 NC_009009:SSA_1226|3end_ParC,_putative_1248783..1248933_NEGATIVE 245 59 11 84 38 NC_009009:SSA_0837|3end_Glucosyltransferase,_putative_825502..825652_POSITIVE 240 58 11 96 53 NC_009009:SSA_1253|3end_hypothetical_protein_1280976..1281126_NEGATIVE