Origin IGS: caggcgcagatggcgttcattagaaccaaaaagatgaaaggcatcatctggatggcccagtttcaattctactgaatgttcctgcaaacaaagaacctctctattttatttttttgaatgaattatctttattatatcaaagcaagcagaaaatgactatccctagccactatccac .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gtggatagtggctagggatagtcattttctgcttgctttgatataataaagataattcattcaaaaaaataaaatagagaggttctttgtttgcaggaacattcagtagaattgaaactgggccatccagatgatgcctttcatctttttggttctaatgaacgccatctgcgcctg Mask Tandem Repeat Region ================================================ caggcgcagatggcgttcattagaaccaaaaagatgaaaggcatcatctggatggcccagtttcaattctactgaatgttcctgcaaacaaagaacctctctattttatttttttgaatgaattatctttattatatcaaagcaagcagaaaatgactatccctagccactatccac Find is-nt database================================================ Query_seq: SSA_1616:SSA_1617|SSA_1616:SSA_1617:PhoH-like protein, putative:hypothetical protein:<-<-:1620349..1620525 177 caggcgcagatggcgttcattagaaccaaaaagatgaaaggcatcatctggatggcccagtttcaattctactgaatgttcctgcaaacaaagaacctctctattttatttttttgaatgaattatctttattatatcaaagcaagcagaaaatgactatccctagccactatccac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1616:SSA_1617|SSA_1616:SSA_1617:PhoH-like protein, putative:hypothetical protein:<-<-:1620349..1620525 177 caggcgcagatggcgttcattagaaccaaaaagatgaaaggcatcatctggatggcccagtttcaattctactgaatgttcctgcaaacaaagaacctctctattttatttttttgaatgaattatctttattatatcaaagcaagcagaaaatgactatccctagccactatccac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1616:SSA_1617|SSA_1616:SSA_1617:PhoH-like protein, putative:hypothetical protein:<-<-:1620349..1620525 177 caggcgcagatggcgttcattagaaccaaaaagatgaaaggcatcatctggatggcccagtttcaattctactgaatgttcctgcaaacaaagaacctctctattttatttttttgaatgaattatctttattatatcaaagcaagcagaaaatgactatccctagccactatccac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 caggcgcagatggcgttcattagaaccaaaaagatgaaaggcatcatctggatggcccagtttcaattctactgaatgttcctgcaaacaaagaacctctctattttatttttttgaatgaattatctttattatatcaaagcaagcagaaaatgactatccctagccactatccac Predict ORF larger than 30AA ================================================ Protein_Len: 43 Strand: + Start: 48 End: 176 ............................................... M D G P V S I L L N V P A N K E P L Y F I F L N E L S L L Y Q S K Q K M T I P S H Y P . caggcgcagatggcgttcattagaaccaaaaagatgaaaggcatcatctggatggcccagtttcaattctactgaatgttcctgcaaacaaagaacctctctattttatttttttgaatgaattatctttattatatcaaagcaagcagaaaatgactatccctagccactatccac 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: 84 Start: 131 End: 160 ..................................................................................................................................ATAGTCATTTTCTGCTTGCTTTGATATAAT................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ caggcgcagatggcgttcattagaaccaaaaagatgaaaggcatcatctggatggcccagtttcaattctactgaatgttcctgcaaacaaagaacctctctattttatttttttgaatgaattatctttattatatcaaagcaagcagaaaatgactatccctagccactatccac Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 70 HP_score: -3.4 Tail_Score: -4.94972 Start: 33 End: 45 Full_Region: ctgggccatccagat gatg ccttt catc tttttggttctaatg ................................gatgcctttcatc.................................................................................................................................... Find igs database================================================ Query_seq: SSA_1616:SSA_1617|SSA_1616:SSA_1617:PhoH-like protein, putative:hypothetical protein:<-<-:1620349..1620525 177 caggcgcagatggcgttcattagaaccaaaaagatgaaaggcatcatctggatggcccagtttcaattctactgaatgttcctgcaaacaaagaacctctctattttatttttttgaatgaattatctttattatatcaaagcaagcagaaaatgactatccctagccactatccac Intra-Species Hit: Count: 1 Min: 1 Max: 177 Len: 177 Subject: NC_009009_SSA_1616_SSA_1617|PhoH-like protein, putative:hypothetical protein|NEGATIVE:NEGATIVE|[1620349,1620525]|177 HSP 1 e-value: 2.0E-83 bit: 309.0 Len: 177 Query Start:1 Query End:177 Subject Strand: POSITIVE Subject Start: 1 Subject End: 177 caggcgcagatggcgttcattagaaccaaaaagatgaaaggcatcatctggatggcccagtttcaattctactgaatgttcctgcaaacaaagaacctctctattttannnnnnngaatgaattatctttattatatcaaagcaagcagaaaatgactatccctagccactatccac caggcgcagatggcgttcattagaaccaaaaagatgaaaggcatcatctggatggcccagtttcaattctactgaatgttcctgcaaacaaagaacctctctattttatttttttgaatgaattatctttattatatcaaagcaagcagaaaatgactatccctagccactatccac Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CAGGCGCAGAUGGCGUUCAUUAGAACCAAAAAGAUGAAAGGCAUCAUCUGGAUGGCCCAGUUUCAAUUCUACUGAAUGUUCCUGCAAACAAAGAACCUCUCUAUUUUAUUUUUUUGAAUGAAUUAUCUUUAUUAUAUCAAAGCAAGCAGAAAAUGACUAUCCCUAGCCACUAUCCAC ..(((...(((((((((((.(((((.......((((.....))))..((((.....))))......))))).))))))...((((......(((.....)))..(((((((....))))))).......................)))).......)))))....)))......... (-34.50) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUGGAUAGUGGCUAGGGAUAGUCAUUUUCUGCUUGCUUUGAUAUAAUAAAGAUAAUUCAUUCAAAAAAAUAAAAUAGAGAGGUUCUUUGUUUGCAGGAACAUUCAGUAGAAUUGAAACUGGGCCAUCCAGAUGAUGCCUUUCAUCUUUUUGGUUCUAAUGAACGCCAUCUGCGCCUG (..((.((((((((....)))))))).))..)....(((((...................)))))......((((((((.....))))))))(((((..(.((((.((((((..(((..((.....)).(((((......))))).)))..)))))).)))).)...)))))..... (-42.71) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 944 60 11 151 102 NC_009009:SSA_1616|5end_PhoH-like_protein,_putative_1620258..1620488_NEGATIVE 316 58 11 121 61 NC_009009:SSA_1605|5end_Major_facilitator_superfamily_multi-drug_resistance_efflux_pump_pmrA,_putative_1611732..1611962_NEGATIVE 314 75 47 34 3 NC_009009:SSA_1796|5end_Transcription_elongation_factor_GreA,_putative_1778307..1778537_NEGATIVE 298 101 61 89 46 NC_009009:SSA_2054|5end_hypothetical_protein_2057899..2058129_NEGATIVE 294 85 41 76 34 NC_009009:SSA_0485|5end_Porphobilinogen_deaminase,_putative_485732..485962_POSITIVE 292 80 38 219 170 NC_009009:SSA_2062|5end_hypothetical_protein_2063521..2063751_NEGATIVE 292 58 13 231 181 NC_009009:SSA_0791|5end_UDP-N-acetylglucosamine-like_protein,_putative_773345..773575_POSITIVE 290 50 1 208 159 NC_009009:SSA_1736|5end_L-cysteine_desulfhydrase,_putative_1722619..1722849_NEGATIVE 284 47 2 108 60 NC_009009:SSA_1366|5end_Alkaline_D-stereospecific_endopeptidase_precursor,_putative_1383663..1383893_NEGATIVE 282 48 5 61 26 NC_009009:SSA_0847|5end_6-phosphofructokinase,_putative_833372..833602_POSITIVE 277 48 1 181 137 NC_009009:SSA_1712|5end_Arsenate_reductase_(ArsC),_glutaredoxin_family,_putative_1700084..1700314_NEGATIVE 274 75 31 71 24 NC_009009:SSA_2153|5end_ABC-type_transporter_(uncharacterized),_permease_component,_putative_2154664..2154894_NEGATIVE 274 62 30 73 35 NC_009009:SSA_1593|5end_Dipeptidase,_putative_1598054..1598284_NEGATIVE 273 84 42 79 32 NC_009009:SSA_1822|5end_hypothetical_protein_1811125..1811355_NEGATIVE 272 86 41 184 133 NC_009009:SSA_1572|5end_hypothetical_protein_1575908..1576138_NEGATIVE 271 139 92 62 20 NC_009009:SSA_2246|5end_Competence-damage_protein,_putative_2242496..2242726_NEGATIVE 270 77 32 76 27 NC_009009:SSA_0502|5end_Peptide_ABC_transporter,_permease_protein,_putative_501554..501784_POSITIVE 269 86 41 224 169 NC_009009:SSA_1606|5end_Dephospho-CoA_kinase,_putative_1612425..1612655_NEGATIVE 267 60 11 70 12 NC_009009:SSA_0339|5end_hypothetical_protein_333950..334180_NEGATIVE 266 67 40 73 41 NC_009009:SSA_1865|5end_Thioredoxin_reductase,_putative_1861892..1862122_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 298 101 61 52 9 NC_009009:SSA_2055|3end_hypothetical_protein_2057936..2058086_NEGATIVE 294 85 41 89 47 NC_009009:SSA_0484|3end_Glutamyl-tRNA_reductase,_putative_485825..485975_POSITIVE 292 80 38 124 75 NC_009009:SSA_2063|3end_Aminopeptidase_PepS,_putative_2063616..2063766_NEGATIVE 291 64 22 71 30 NC_009009:SSA_0704|3end_Isocitrate_dehydrogenase_[NADP],_putative_690550..690700_POSITIVE 277 48 1 56 12 NC_009009:SSA_1713|3end_D-3-phosphoglycerate_dehydrogenase,_putative_1700209..1700359_NEGATIVE 273 84 42 52 5 NC_009009:SSA_1823|3end_hypothetical_protein_1811152..1811302_NEGATIVE 267 60 11 65 7 NC_009009:SSA_0341|3end_hypothetical_protein_333955..334105_NEGATIVE 257 168 126 87 46 NC_009009:SSA_2301|3end_S-layer_protein/_peptidoglycan_endo-beta-N-acetylglucosaminidase,_putative_2302669..2302819_NEGATIVE 256 49 1 92 60 NC_009009:SSA_0294|3end_hypothetical_protein_287772..287922_NEGATIVE 254 85 41 76 33 NC_009009:SSA_0239|3end_7,8-dihydro-8-oxoguanine-triphosphatase,_putative_233493..233643_POSITIVE 252 50 1 56 5 NC_009009:SSA_0039|3end_Phosphoribosylaminoimidazole_carboxylase,_catalytic_subunit,_putative_46401..46551_POSITIVE 251 85 41 143 102 NC_009009:SSA_0335|3end_Phosphomevalonate_kinase,_putative_329891..330041_POSITIVE 250 84 46 106 66 NC_009009:SSA_1800|3end_UDP-N-acetylmuramate--L-alanine_ligase,_putative_1781037..1781187_NEGATIVE 246 70 21 84 25 NC_009009:SSA_0734|3end_Arsenical_resistance_operon_transcription_repressor_(ArsR),_putative_717196..717346_POSITIVE 245 83 41 77 32 NC_009009:SSA_1198|3end_ATPase_(PilT_family),_putative_1222703..1222853_NEGATIVE 245 71 31 87 53 NC_009009:SSA_0303|3end_surface_protein_C_301051..301201_POSITIVE 241 90 41 61 6 NC_009009:SSA_1340|3end_Zn/Mn_ABC-type_porter_lipoprotein,_putative_1355434..1355584_NEGATIVE 241 41 2 143 107 NC_009009:SSA_1157|3end_PvaA-like_protein,_putative_1186218..1186368_POSITIVE 241 60 12 86 32 NC_009009:SSA_0451|3end_Conserved_uncharacterized_protein_451636..451786_POSITIVE 240 50 2 96 39 NC_009009:SSA_2263|3end_Ribonucleotide_reductase_(NrdI_family_protein),_putative_2260688..2260838_NEGATIVE