Origin IGS: aataggcttgaagaaatttcgccaatgaactagaagaatttcaggagggcgcaaaaacaggtagaacttatgttctacctgttttgttatcaaaaaattcttgaaagtgatggagataatagaaagcttcagctagctaatgactgtcctgctcctaagtcagtttgatagttaaagagggtaact .........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 agttaccctctttaactatcaaactgacttaggagcaggacagtcattagctagctgaagctttctattatctccatcactttcaagaattttttgataacaaaacaggtagaacataagttctacctgtttttgcgccctcctgaaattcttctagttcattggcgaaatttcttcaagcctatt Mask Tandem Repeat Region ================================================ aataggcttgaagaaatttcgccaatgaactagaagaatttcaggagggcgcaaaaacaggtagaacttatgttctacctgttttgttatcaaaaaattcttgaaagtgatggagataatagaaagcttcagctagctaatgactgtcctgctcctaagtcagtttgatagttaaagagggtaact Find is-nt database================================================ Query_seq: SSA_0906:SSA_0907|SSA_0906:SSA_0907:CshA-like fibrillar surface protein C:Fibronectin-binding protein A, putative:-><-:917472..917657 186 aataggcttgaagaaatttcgccaatgaactagaagaatttcaggagggcgcaaaaacaggtagaacttatgttctacctgttttgttatcaaaaaattcttgaaagtgatggagataatagaaagcttcagctagctaatgactgtcctgctcctaagtcagtttgatagttaaagagggtaact Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0906:SSA_0907|SSA_0906:SSA_0907:CshA-like fibrillar surface protein C:Fibronectin-binding protein A, putative:-><-:917472..917657 186 aataggcttgaagaaatttcgccaatgaactagaagaatttcaggagggcgcaaaaacaggtagaacttatgttctacctgttttgttatcaaaaaattcttgaaagtgatggagataatagaaagcttcagctagctaatgactgtcctgctcctaagtcagtttgatagttaaagagggtaact Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0906:SSA_0907|SSA_0906:SSA_0907:CshA-like fibrillar surface protein C:Fibronectin-binding protein A, putative:-><-:917472..917657 186 aataggcttgaagaaatttcgccaatgaactagaagaatttcaggagggcgcaaaaacaggtagaacttatgttctacctgttttgttatcaaaaaattcttgaaagtgatggagataatagaaagcttcagctagctaatgactgtcctgctcctaagtcagtttgatagttaaagagggtaact Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aataggcttgaagaaatttcgccaatgaactagaagaatttcaggagggcgcaaaaacaggtagaacttatgttctacctgttttgttatcaaaaaattcttgaaagtgatggagataatagaaagcttcagctagctaatgactgtcctgctcctaagtcagtttgatagttaaagagggtaact Predict ORF larger than 30AA ================================================ Protein_Len: 32 Strand: + Start: 70 End: 165 ..................................................................... M F Y L F C Y Q K I L E S D G D N R K L Q L A N D C P A P K S V ..................... Protein_Len: 44 Strand: - Start: 1 End: 132 I P K F F N R W H V L L I E P P R L F L Y F K H E V Q K T I L F N K F T I S I I S L K M ...................................................... aataggcttgaagaaatttcgccaatgaactagaagaatttcaggagggcgcaaaaacaggtagaacttatgttctacctgttttgttatcaaaaaattcttgaaagtgatggagataatagaaagcttcagctagctaatgactgtcctgctcctaagtcagtttgatagttaaagagggtaact Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aataggcttgaagaaatttcgccaatgaactagaagaatttcaggagggcgcaaaaacaggtagaacttatgttctacctgttttgttatcaaaaaattcttgaaagtgatggagataatagaaagcttcagctagctaatgactgtcctgctcctaagtcagtttgatagttaaagagggtaact Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 100 HP_score: -14.1 Tail_Score: -3.30338 Start: 53 End: 86 Full_Region: ATTTCAGGAGGGCGC AAAAACAGGTAGAAC TTAT GTTCTACCTGTTTTG TTATCAAAAAATTCT ....................................................AAAAACAGGTAGAACTTATGTTCTACCTGTTTTG.................................................................................................... TransTerm Strand: + Conf: 100 HP_score: -14.0 Tail_Score: -4.77165 Start: 58 End: 81 Full_Region: AGGAGGGCGCAAAAA CAGGTAGAAC TTAT GTTCTACCTG TTTTGTTATCAAAAA .........................................................CAGGTAGAACTTATGTTCTACCTG......................................................................................................... TransTerm Strand: - Conf: 100 HP_score: -14.0 Tail_Score: -4.58663 Start: 58 End: 81 Full_Region: tttttgataacaaaa caggtagaac ataa gttctacctg tttttgcgccctcct .........................................................caggtagaacataagttctacctg......................................................................................................... Find igs database================================================ Query_seq: SSA_0906:SSA_0907|SSA_0906:SSA_0907:CshA-like fibrillar surface protein C:Fibronectin-binding protein A, putative:-><-:917472..917657 186 aataggcttgaagaaatttcgccaatgaactagaagaatttcaggagggcgcaaaaacaggtagaacttatgttctacctgttttgttatcaaaaaattcttgaaagtgatggagataatagaaagcttcagctagctaatgactgtcctgctcctaagtcagtttgatagttaaagagggtaact Intra-Species Hit: Count: 1 Min: 1 Max: 186 Len: 186 Subject: NC_009009_SSA_0906_SSA_0907|CshA-like fibrillar surface protein C:Fibronectin-binding protein A, putative|POSITIVE:NEGATIVE|[917472,917657]|186 HSP 1 e-value: 1.0E-101 bit: 369.0 Len: 186 Query Start:1 Query End:186 Subject Strand: POSITIVE Subject Start: 1 Subject End: 186 aataggcttgaagaaatttcgccaatgaactagaagaatttcaggagggcgcaaaaacaggtagaacttatgttctacctgttttgttatcaaaaaattcttgaaagtgatggagataatagaaagcttcagctagctaatgactgtcctgctcctaagtcagtttgatagttaaagagggtaact aataggcttgaagaaatttcgccaatgaactagaagaatttcaggagggcgcaaaaacaggtagaacttatgttctacctgttttgttatcaaaaaattcttgaaagtgatggagataatagaaagcttcagctagctaatgactgtcctgctcctaagtcagtttgatagttaaagagggtaact Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUAGGCUUGAAGAAAUUUCGCCAAUGAACUAGAAGAAUUUCAGGAGGGCGCAAAAACAGGUAGAACUUAUGUUCUACCUGUUUUGUUAUCAAAAAAUUCUUGAAAGUGAUGGAGAUAAUAGAAAGCUUCAGCUAGCUAAUGACUGUCCUGCUCCUAAGUCAGUUUGAUAGUUAAAGAGGGUAACU ....((((.((((...((((.(((....(((..((((((((...((..(((...(((((((((((((....))))))))))))))))..))...))))))))...)))..)))........)))).))))))))..((..((((((((..(((........)))..))))))))...))....... (-52.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGUUACCCUCUUUAACUAUCAAACUGACUUAGGAGCAGGACAGUCAUUAGCUAGCUGAAGCUUUCUAUUAUCUCCAUCACUUUCAAGAAUUUUUUGAUAACAAAACAGGUAGAACAUAAGUUCUACCUGUUUUUGCGCCCUCCUGAAAUUCUUCUAGUUCAUUGGCGAAAUUUCUUCAAGCCUAUU (((((.......))))).......(((.((((((((((((..((...(((..(((....)))..)))...............((((((...))))))....((((((((((((((....))))))))))))))...))..))))).....))))))).)))..(((.............))).... (-42.82) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 349 170 121 67 12 NC_009009:SSA_0620|5end_hypothetical_protein_612325..612555_NEGATIVE 347 166 126 49 1 NC_009009:SSA_2171|5end_hypothetical_protein_2170760..2170990_NEGATIVE 338 169 125 73 8 NC_009009:SSA_1325|5end_Ketoacyl_reductase_hetN,_putative_1342343..1342573_NEGATIVE 324 165 122 65 23 NC_009009:SSA_0900|5end_Tetratricopeptide_repeat_(TPR)_family_protein_891068..891298_POSITIVE 323 168 121 78 16 NC_009009:SSA_1913|5end_Xanthine/uracil_permease_family_protein,_putative_1904666..1904896_NEGATIVE 322 178 131 214 171 NC_009009:SSA_1448|5end_ATP_phosphoribosyltransferase_regulatory_subunit,_putative_1450817..1451047_NEGATIVE 307 180 132 230 185 NC_009009:SSA_1401|5end_Transcriptional_regulator_GntR_family_1413062..1413292_POSITIVE 301 49 3 163 108 NC_009009:SSA_1264|5end_hypothetical_protein_1290042..1290272_NEGATIVE 297 162 125 189 152 NC_009009:SSA_1483|5end_Sphingosine_kinase_(diacylglycerol_kinase),_putative_1490220..1490450_NEGATIVE 297 168 125 72 14 NC_009009:SSA_0087|5end_V-type_sodium_ATPase,_subunit_E,_putative_88329..88559_POSITIVE 296 159 125 156 110 NC_009009:SSA_0582|5end_Methylase,_putative_573769..573999_POSITIVE 295 167 121 71 17 NC_009009:SSA_0487|5end_Delta-aminolevulinic_acid_dehydratase,_putative_487349..487579_POSITIVE 292 180 132 84 33 NC_009009:SSA_0814|5end_Oxidoreductase,_pyridine_nucleotide-disulfide,_class_I,_putative_796835..797065_NEGATIVE 291 180 131 57 16 NC_009009:SSA_1454|5end_hypothetical_protein_1461100..1461330_NEGATIVE 290 169 121 202 138 NC_009009:SSA_0987|5end_ABC-type_choline_transporter,_membrane-spanning_permease,_putative_988994..989224_POSITIVE 289 163 123 70 14 NC_009009:SSA_1447|5end_ATP_phosphoribosyltransferase,_putative_1449831..1450061_NEGATIVE 287 170 126 62 24 NC_009009:SSA_2359|5end_Glucose_inhibited_division_protein_A,_putative_2362520..2362750_NEGATIVE 283 173 138 51 7 NC_009009:SSA_0539|5end_PduO_protein,_putative_534233..534463_POSITIVE 280 155 126 212 184 NC_009009:SSA_2239|5end_Conserved_uncharacterized_cytosolic_protein_2237233..2237463_NEGATIVE 280 170 126 57 17 NC_009009:SSA_0918|5end_Conserved_uncharacterized_protein_930398..930628_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 349 170 121 70 15 NC_009009:SSA_0621|3end_SOS_responce_UmuC_protein,_putative_612322..612472_NEGATIVE 348 85 54 37 6 NC_009009:SSA_0906|3end_CshA-like_fibrillar_surface_protein_C_917411..917561_POSITIVE 324 165 122 78 36 NC_009009:SSA_0899|3end_Conserved_permease,_putative_891161..891311_POSITIVE 297 168 125 61 3 NC_009009:SSA_0086|3end_V-type_sodium_ATPase,_subunit_K,_putative_88398..88548_POSITIVE 296 159 125 81 35 NC_009009:SSA_0581|3end_Conserved_uncharacterized_protein_573774..573924_POSITIVE 295 167 121 84 30 NC_009009:SSA_0486|3end_Uroporphyrinogen-III_synthase,_putative_487442..487592_POSITIVE 290 65 25 145 106 NC_009009:SSA_2170|3end_hypothetical_protein_2169557..2169707_NEGATIVE 289 163 123 73 17 NC_009009:SSA_1448|3end_ATP_phosphoribosyltransferase_regulatory_subunit,_putative_1449828..1449978_NEGATIVE 275 163 125 128 74 NC_009009:SSA_2178|3end_hypothetical_protein_2176288..2176438_NEGATIVE 274 168 126 65 5 NC_009009:SSA_0197|3end_Dihydropteroate_synthase,_putative_196979..197129_POSITIVE 272 167 127 151 108 NC_009009:SSA_1449|3end_Histidinol-phosphate/aromatic_aminotransferase_and_cobyric_acid_decarboxylase,_putative_1450873..1451023_NEGATIVE 271 166 123 46 1 NC_009009:SSA_0345|3end_hypothetical_protein_339209..339359_POSITIVE 268 50 1 88 38 NC_009009:SSA_0478|3end_Cobalt_transport_protein_cbiN,_putative_480387..480537_POSITIVE 267 169 128 150 98 NC_009009:SSA_2346|3end_3-oxoacyl-[acyl-carrier-protein]_synthase_III,_putative_2347602..2347752_NEGATIVE 265 173 131 74 35 NC_009009:SSA_0531|3end_Ethanolamine_utilization_protein_eutQ_(cobalamin-dependent_degradation_of_ethanolamine),_putative_527884..528034_POSITIVE 263 156 114 112 65 NC_009009:SSA_1593|3end_Dipeptidase,_putative_1596390..1596540_NEGATIVE 262 169 121 69 19 NC_009009:SSA_1935|3end_Beta-ketoacyl-ACP_synthase_II_(3-oxoacyl-(Acyl-carrier-protein)_synthase_II),_putative_1921807..1921957_NEGATIVE 261 88 41 62 11 NC_009009:SSA_0387|3end_Transcriptional_regulator,_GntR_family,_putative_381702..381852_NEGATIVE 258 165 125 56 24 NC_009009:SSA_0271|3end_Glycosylhydrolase,_family_35,_putative_266093..266243_POSITIVE 256 165 125 143 106 NC_009009:SSA_0833|3end_Accessory_secretory_protein_Asp1,_putative_819600..819750_POSITIVE