Origin IGS: ctgcgaggatgattaggagctttttggagcctcaaagacgaacaaagttgtgactcgcttcgcaaattctatctgcaacttcaaagcagcaatttgacaatcggctattgcgtcaagattctatttctaataaaaagcaaggctagaacttatgtctcttagcctttttctatgtgttttagcaaggcatgttcgcaggatatcatctgaacttagagacgttgatacctagtcaagtacagcacttagcaagatcagatattttaaggacaaccccttatatacttatgctattattttacaggccaattctcttttgatataatgaaagcagaataaagccttgtacaaagagattcaaagagttctgaaggatttacaatataggtaaattcgtcataagtctgtagtatcgaaatctttaaggggtattactttgtgggtagggtagatttttaggaggtctt .........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.........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 aagacctcctaaaaatctaccctacccacaaagtaataccccttaaagatttcgatactacagacttatgacgaatttacctatattgtaaatccttcagaactctttgaatctctttgtacaaggctttattctgctttcattatatcaaaagagaattggcctgtaaaataatagcataagtatataaggggttgtccttaaaatatctgatcttgctaagtgctgtacttgactaggtatcaacgtctctaagttcagatgatatcctgcgaacatgccttgctaaaacacatagaaaaaggctaagagacataagttctagccttgctttttattagaaatagaatcttgacgcaatagccgattgtcaaattgctgctttgaagttgcagatagaatttgcgaagcgagtcacaactttgttcgtctttgaggctccaaaaagctcctaatcatcctcgcag Mask Tandem Repeat Region ================================================ ctgcgaggatgattaggagctttttggagcctcaaagacgaacaaagttgtgactcgcttcgcaaattctatctgcaacttcaaagcagcaatttgacaatcggctattgcgtcaagattctatttctaataaaaagcaaggctagaacttatgtctcttagcctttttctatgtgttttagcaaggcatgttcgcaggatatcatctgaacttagagacgttgatacctagtcaagtacagcacttagcaagatcagatattttaaggacaaccccttatatacttatgctattattttacaggccaattctcttttgatataatgaaagcagaataaagccttgtacaaagagattcaaagagttctgaaggatttacaatataggtaaattcgtcataagtctgtagtatcgaaatctttaaggggtattactttgtgggtagggtagatttttaggaggtctt Find is-nt database================================================ Query_seq: SSA_0686:SSA_0687|SSA_0686:SSA_0687:Fe2+/Zn2+ uptake regulation protein, putative:hypothetical protein:->->:670140..670606 467 ctgcgaggatgattaggagctttttggagcctcaaagacgaacaaagttgtgactcgcttcgcaaattctatctgcaacttcaaagcagcaatttgacaatcggctattgcgtcaagattctatttctaataaaaagcaaggctagaacttatgtctcttagcctttttctatgtgttttagcaaggcatgttcgcaggatatcatctgaacttagagacgttgatacctagtcaagtacagcacttagcaagatcagatattttaaggacaaccccttatatacttatgctattattttacaggccaattctcttttgatataatgaaagcagaataaagccttgtacaaagagattcaaagagttctgaaggatttacaatataggtaaattcgtcataagtctgtagtatcgaaatctttaaggggtattactttgtgggtagggtagatttttaggaggtctt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0686:SSA_0687|SSA_0686:SSA_0687:Fe2+/Zn2+ uptake regulation protein, putative:hypothetical protein:->->:670140..670606 467 ctgcgaggatgattaggagctttttggagcctcaaagacgaacaaagttgtgactcgcttcgcaaattctatctgcaacttcaaagcagcaatttgacaatcggctattgcgtcaagattctatttctaataaaaagcaaggctagaacttatgtctcttagcctttttctatgtgttttagcaaggcatgttcgcaggatatcatctgaacttagagacgttgatacctagtcaagtacagcacttagcaagatcagatattttaaggacaaccccttatatacttatgctattattttacaggccaattctcttttgatataatgaaagcagaataaagccttgtacaaagagattcaaagagttctgaaggatttacaatataggtaaattcgtcataagtctgtagtatcgaaatctttaaggggtattactttgtgggtagggtagatttttaggaggtctt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0686:SSA_0687|SSA_0686:SSA_0687:Fe2+/Zn2+ uptake regulation protein, putative:hypothetical protein:->->:670140..670606 467 ctgcgaggatgattaggagctttttggagcctcaaagacgaacaaagttgtgactcgcttcgcaaattctatctgcaacttcaaagcagcaatttgacaatcggctattgcgtcaagattctatttctaataaaaagcaaggctagaacttatgtctcttagcctttttctatgtgttttagcaaggcatgttcgcaggatatcatctgaacttagagacgttgatacctagtcaagtacagcacttagcaagatcagatattttaaggacaaccccttatatacttatgctattattttacaggccaattctcttttgatataatgaaagcagaataaagccttgtacaaagagattcaaagagttctgaaggatttacaatataggtaaattcgtcataagtctgtagtatcgaaatctttaaggggtattactttgtgggtagggtagatttttaggaggtctt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ctgcgaggatgattaggagctttttggagcctcaaagacgaacaaagttgtgactcgcttcgcaaattctatctgcaacttcaaagcagcaatttgacaatcggctattgcgtcaagattctatttctaataaaaagcaaggctagaacttatgtctcttagcctttttctatgtgttttagcaaggcatgttcgcaggatatcatctgaacttagagacgttgatacctagtcaagtacagcacttagcaagatcagatattttaaggacaaccccttatatacttatgctattattttacaggccaattctcttttgatataatgaaagcagaataaagccttgtacaaagagattcaaagagttctgaaggatttacaatataggtaaattcgtcataagtctgtagtatcgaaatctttaaggggtattactttgtgggtagggtagatttttaggaggtctt Predict ORF larger than 30AA ================================================ Protein_Len: 43 Strand: + Start: 189 End: 317 ............................................................................................................................................................................................ M F A G Y H L N L E T L I P S Q V Q H L A R S D I L R T T P Y I L M L L F Y R P I L F ...................................................................................................................................................... Protein_Len: 41 Strand: - Start: 297 End: 419 ........................................................................................................................................................................................................................................................................................................ K V P W N E K S I I F A S Y L R T C L S E F L E S P N V I Y T F E D Y T Q L I S M ................................................ Protein_Len: 31 Strand: - Start: 16 End: 108 ............... S S K P A E F V F L T T V R K A F E I Q L K L A A I Q C D A M ....................................................................................................................................................................................................................................................................................................................................................................... ctgcgaggatgattaggagctttttggagcctcaaagacgaacaaagttgtgactcgcttcgcaaattctatctgcaacttcaaagcagcaatttgacaatcggctattgcgtcaagattctatttctaataaaaagcaaggctagaacttatgtctcttagcctttttctatgtgttttagcaaggcatgttcgcaggatatcatctgaacttagagacgttgatacctagtcaagtacagcacttagcaagatcagatattttaaggacaaccccttatatacttatgctattattttacaggccaattctcttttgatataatgaaagcagaataaagccttgtacaaagagattcaaagagttctgaaggatttacaatataggtaaattcgtcataagtctgtagtatcgaaatctttaaggggtattactttgtgggtagggtagatttttaggaggtctt 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: 86 Start: 297 End: 326 ........................................................................................................................................................................................................................................................................................................TTTTACAGGCCAATTCTCTTTTGATATAAT............................................................................................................................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ ctgcgaggatgattaggagctttttggagcctcaaagacgaacaaagttgtgactcgcttcgcaaattctatctgcaacttcaaagcagcaatttgacaatcggctattgcgtcaagattctatttctaataaaaagcaaggctagaacttatgtctcttagcctttttctatgtgttttagcaaggcatgttcgcaggatatcatctgaacttagagacgttgatacctagtcaagtacagcacttagcaagatcagatattttaaggacaaccccttatatacttatgctattattttacaggccaattctcttttgatataatgaaagcagaataaagccttgtacaaagagattcaaagagttctgaaggatttacaatataggtaaattcgtcataagtctgtagtatcgaaatctttaaggggtattactttgtgggtagggtagatttttaggaggtctt Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 45 HP_score: -3.3 Tail_Score: -2.99188 Start: 265 End: 280 Full_Region: CAAGATCAGATATTT TAAGG ACAACC CCTTA TATACTTATGCTATT ........................................................................................................................................................................................................................................................................TAAGGACAACCCCTTA........................................................................................................................................................................................... Find igs database================================================ Query_seq: SSA_0686:SSA_0687|SSA_0686:SSA_0687:Fe2+/Zn2+ uptake regulation protein, putative:hypothetical protein:->->:670140..670606 467 ctgcgaggatgattaggagctttttggagcctcaaagacgaacaaagttgtgactcgcttcgcaaattctatctgcaacttcaaagcagcaatttgacaatcggctattgcgtcaagattctatttctaataaaaagcaaggctagaacttatgtctcttagcctttttctatgtgttttagcaaggcatgttcgcaggatatcatctgaacttagagacgttgatacctagtcaagtacagcacttagcaagatcagatattttaaggacaaccccttatatacttatgctattattttacaggccaattctcttttgatataatgaaagcagaataaagccttgtacaaagagattcaaagagttctgaaggatttacaatataggtaaattcgtcataagtctgtagtatcgaaatctttaaggggtattactttgtgggtagggtagatttttaggaggtctt Intra-Species Hit: Count: 1 Min: 1 Max: 467 Len: 467 Subject: NC_009009_SSA_0686_SSA_0687|Fe2+/Zn2+ uptake regulation protein, putative:hypothetical protein|POSITIVE:POSITIVE|[670140,670606]|467 HSP 1 e-value: 0.0 bit: 926.0 Len: 467 Query Start:1 Query End:467 Subject Strand: POSITIVE Subject Start: 1 Subject End: 467 ctgcgaggatgattaggagctttttggagcctcaaagacgaacaaagttgtgactcgcttcgcaaattctatctgcaacttcaaagcagcaatttgacaatcggctattgcgtcaagattctatttctaataaaaagcaaggctagaacttatgtctcttagcctttttctatgtgttttagcaaggcatgttcgcaggatatcatctgaacttagagacgttgatacctagtcaagtacagcacttagcaagatcagatattttaaggacaaccccttatatacttatgctattattttacaggccaattctcttttgatataatgaaagcagaataaagccttgtacaaagagattcaaagagttctgaaggatttacaatataggtaaattcgtcataagtctgtagtatcgaaatctttaaggggtattactttgtgggtagggtagatttttaggaggtctt ctgcgaggatgattaggagctttttggagcctcaaagacgaacaaagttgtgactcgcttcgcaaattctatctgcaacttcaaagcagcaatttgacaatcggctattgcgtcaagattctatttctaataaaaagcaaggctagaacttatgtctcttagcctttttctatgtgttttagcaaggcatgttcgcaggatatcatctgaacttagagacgttgatacctagtcaagtacagcacttagcaagatcagatattttaaggacaaccccttatatacttatgctattattttacaggccaattctcttttgatataatgaaagcagaataaagccttgtacaaagagattcaaagagttctgaaggatttacaatataggtaaattcgtcataagtctgtagtatcgaaatctttaaggggtattactttgtgggtagggtagatttttaggaggtctt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUGCGAGGAUGAUUAGGAGCUUUUUGGAGCCUCAAAGACGAACAAAGUUGUGACUCGCUUCGCAAAUUCUAUCUGCAACUUCAAAGCAGCAAUUUGACAAUCGGCUAUUGCGUCAAGAUUCUAUUUCUAAUAAAAAGCAAGGCUAGAACUUAUGUCUCUUAGCCUUUUUCUAUGUGUUUUAGCAAGGCAUGUUCGCAGGAUAUCAUCUGAACUUAGAGACGUUGAUACCUAGUCAAGUACAGCACUUAGCAAGAUCAGAUAUUUUAAGGACAACCCCUUAUAUACUUAUGCUAUUAUUUUACAGGCCAAUUCUCUUUUGAUAUAAUGAAAGCAGAAUAAAGCCUUGUACAAAGAGAUUCAAAGAGUUCUGAAGGAUUUACAAUAUAGGUAAAUUCGUCAUAAGUCUGUAGUAUCGAAAUCUUUAAGGGGUAUUACUUUGUGGGUAGGGUAGAUUUUUAGGAGGUCUU .(((((((.(((...(..((((....))))..)....((((......))))...)))))))))).((((((((..(((.............((((((......((((.(((....(((.......)))............((((((.....((((((((..(((((...(((.......))).)))))..(((((...(....)...)))))..))))))))......)))))).......)))..))))....))))))............((((((((.......(((((((.....(((((((..((((((((((........))))).)))))...))).)))).............(((.((.(((.((((((((.......)))))))).))).)).)))))))))).........))))))))......)))..)))))))).((((((...)))))).. (-112.19) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAGACCUCCUAAAAAUCUACCCUACCCACAAAGUAAUACCCCUUAAAGAUUUCGAUACUACAGACUUAUGACGAAUUUACCUAUAUUGUAAAUCCUUCAGAACUCUUUGAAUCUCUUUGUACAAGGCUUUAUUCUGCUUUCAUUAUAUCAAAAGAGAAUUGGCCUGUAAAAUAAUAGCAUAAGUAUAUAAGGGGUUGUCCUUAAAAUAUCUGAUCUUGCUAAGUGCUGUACUUGACUAGGUAUCAACGUCUCUAAGUUCAGAUGAUAUCCUGCGAACAUGCCUUGCUAAAACACAUAGAAAAAGGCUAAGAGACAUAAGUUCUAGCCUUGCUUUUUAUUAGAAAUAGAAUCUUGACGCAAUAGCCGAUUGUCAAAUUGCUGCUUUGAAGUUGCAGAUAGAAUUUGCGAAGCGAGUCACAACUUUGUUCGUCUUUGAGGCUCCAAAAAGCUCCUAAUCAUCCUCGCAG ..............................(((....((((((((..(....)..........(((((((.(..((((((.......))))))..((((((....))))))........((((.((((..(((((.((((..........))))))))).))))))))........))))))))...))))))))....)))....(((((((.((((....((...(((((......)))))..)).....)))).))))))).....((((((..(((.....................(((((((.(((.(....)))))))))))(((((((...............(((((((....)).....)))))......((((..(((((((((((...)))))))).(((((.((......))))))))))..))))...))))))).......)))..)))))) (-94.00) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 470 41 1 173 133 NC_009009:SSA_2300|5end_hypothetical_protein_2302508..2302738_NEGATIVE 317 170 126 146 109 NC_009009:SSA_1307|5end_Trk_transporter_membrane-spanning_protein-K+_transport,_putative_1326270..1326500_NEGATIVE 309 98 54 95 48 NC_009009:SSA_1575|5end_Glycosyl_transferase,_putative_1579110..1579340_NEGATIVE 306 90 44 228 183 NC_009009:SSA_1268|5end_Chorismate_mutase/prephenate_dehydratase,_putative_1291610..1291840_NEGATIVE 304 199 157 145 91 NC_009009:SSA_2080|5end_hypothetical_protein_2085341..2085571_NEGATIVE 304 90 46 197 159 NC_009009:SSA_0220|5end_PTS_system,_mannose-specific_IIB_component,_putative_215848..216078_POSITIVE 297 200 151 133 91 NC_009009:SSA_2062|5end_hypothetical_protein_2063521..2063751_NEGATIVE 297 114 72 210 162 NC_009009:SSA_0680|5end_Serine/threonine_protein_phosphatase,_putative_662425..662655_POSITIVE 296 230 182 82 38 NC_009009:SSA_2118|5end_Thiamine_pyrophosphokinase,_putative_2120500..2120730_NEGATIVE 296 120 74 65 20 NC_009009:SSA_0478|5end_Cobalt_transport_protein_cbiN,_putative_480002..480232_POSITIVE 294 200 160 36 7 NC_009009:SSA_0898|5end_hypothetical_protein_889863..890093_NEGATIVE 291 170 124 223 183 NC_009009:SSA_1997|5end_Membrane_spanning_protein,_putative_1994911..1995141_NEGATIVE 291 98 52 211 164 NC_009009:SSA_0929|5end_ABC-type_multidrug_transporter,_ATPase_and_permease_components,_putative_938438..938668_POSITIVE 286 200 153 151 86 NC_009009:SSA_0647|5end_hypothetical_protein_630998..631228_POSITIVE 282 121 82 97 65 NC_009009:SSA_0941|5end_ABC-type_phosphate_transport_system,_periplasmic_component,_putative_949157..949387_POSITIVE 282 54 11 64 13 NC_009009:SSA_0565|5end_hypothetical_protein_557230..557460_POSITIVE 279 350 303 208 160 NC_009009:SSA_0908|5end_ABC-type_uncharacterized_transport_system,_periplasmic_component,_putative_919700..919930_POSITIVE 278 259 228 71 35 NC_009009:SSA_1984|5end_Cell_surface_SD_repeat_antigen_precursor,_putative_1979035..1979265_NEGATIVE 278 120 71 203 150 NC_009009:SSA_0773|5end_PTS_enzyme_I,_putative_752603..752833_POSITIVE 278 210 165 172 128 NC_009009:SSA_0104|5end_Queuine_tRNA-ribosyltransferase,_putative_105593..105823_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 338 179 134 73 30 NC_009009:SSA_1162|3end_Possible_fimbrial_assembly_protein_fimC,_putative_1188489..1188639_NEGATIVE 317 170 126 149 112 NC_009009:SSA_1308|3end_hypothetical_protein_1326267..1326417_NEGATIVE 316 91 54 121 77 NC_009009:SSA_0150|3end_hypothetical_protein_145227..145377_POSITIVE 304 199 157 135 81 NC_009009:SSA_2082|3end_Carbohydrate_kinase,_FGGY_family,_putative_2085351..2085501_NEGATIVE 297 166 121 71 26 NC_009009:SSA_1161|3end_hypothetical_protein_1188443..1188593_POSITIVE 296 230 182 143 99 NC_009009:SSA_2119|3end_Pentose-5-phosphate-3-epimerase,_putative_2120439..2120589_NEGATIVE 296 120 74 68 23 NC_009009:SSA_0477|3end_Cobalamin_biosynthesis_protein_CbiM_(ABC-type_cobalt_transporter),_putative_480085..480235_POSITIVE 295 206 163 57 4 NC_009009:SSA_2063|3end_Aminopeptidase_PepS,_putative_2063616..2063766_NEGATIVE 294 200 160 131 102 NC_009009:SSA_0898|3end_hypothetical_protein_889768..889918_NEGATIVE 291 170 124 86 46 NC_009009:SSA_1998|3end_Trigger_factor,_putative_1995048..1995198_NEGATIVE 289 169 124 92 48 NC_009009:SSA_2301|3end_S-layer_protein/_peptidoglycan_endo-beta-N-acetylglucosaminidase,_putative_2302669..2302819_NEGATIVE 288 180 131 101 41 NC_009009:SSA_0099|3end_hypothetical_protein_100134..100284_NEGATIVE 286 200 153 149 84 NC_009009:SSA_0646|3end_hypothetical_protein_631076..631226_POSITIVE 284 257 219 151 113 NC_009009:SSA_1063|3end_Peptidoglycan-binding_domain-containing_protein,_putative_1080260..1080410_POSITIVE 280 173 139 94 59 NC_009009:SSA_0395|3end_6-phospho-beta-glucosidase,_putative_392580..392730_POSITIVE 277 60 14 64 24 NC_009009:SSA_0759|3end_Acetylglutamate_kinase,_putative_742658..742808_POSITIVE 277 200 152 59 5 NC_009009:SSA_0338|3end_Hydroxymethylglutaryl-CoA_synthase,_putative_332160..332310_NEGATIVE 276 189 149 59 15 NC_009009:SSA_1892|3end_hypothetical_protein_1889068..1889218_NEGATIVE 275 218 174 149 113 NC_009009:SSA_2123|3end_Dimethyladenosine_transferase,_putative_2127664..2127814_NEGATIVE 274 244 204 122 82 NC_009009:SSA_1459|3end_RNA_methyltransferase,_putative_1466111..1466261_NEGATIVE