Origin IGS: gtgcaacatttactcgaactcatcctctagagcttcactagcagttctgtaagctaaacattttcgtggtcggtgattgatatcatataaagccttggttcccaaagcttttttatgttataaactca .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tgagtttataacataaaaaagctttgggaaccaaggctttatatgatatcaatcaccgaccacgaaaatgtttagcttacagaactgctagtgaagctctagaggatgagttcgagtaaatgttgcac Mask Tandem Repeat Region ================================================ gtgcaacatttactcgaactcatcctctagagcttcactagcagttctgtaagctaaacattttcgtggtcggtgattgatatcatataaagccttggttcccaaagcttttttatgttataaactca Find is-nt database================================================ Query_seq: SSA_0229:SSA_0230|SSA_0229:SSA_0230:hypothetical protein:hypothetical protein:-><-:223774..223901 128 gtgcaacatttactcgaactcatcctctagagcttcactagcagttctgtaagctaaacattttcgtggtcggtgattgatatcatataaagccttggttcccaaagcttttttatgttataaactca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0229:SSA_0230|SSA_0229:SSA_0230:hypothetical protein:hypothetical protein:-><-:223774..223901 128 gtgcaacatttactcgaactcatcctctagagcttcactagcagttctgtaagctaaacattttcgtggtcggtgattgatatcatataaagccttggttcccaaagcttttttatgttataaactca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0229:SSA_0230|SSA_0229:SSA_0230:hypothetical protein:hypothetical protein:-><-:223774..223901 128 gtgcaacatttactcgaactcatcctctagagcttcactagcagttctgtaagctaaacattttcgtggtcggtgattgatatcatataaagccttggttcccaaagcttttttatgttataaactca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gtgcaacatttactcgaactcatcctctagagcttcactagcagttctgtaagctaaacattttcgtggtcggtgattgatatcatataaagccttggttcccaaagcttttttatgttataaactca Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: - Start: 13 End: 105 ............ E F E D E L A E S A T R Y A L C K R P R H N I D Y L A K T G M ....................... gtgcaacatttactcgaactcatcctctagagcttcactagcagttctgtaagctaaacattttcgtggtcggtgattgatatcatataaagccttggttcccaaagcttttttatgttataaactca 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================================================ gtgcaacatttactcgaactcatcctctagagcttcactagcagttctgtaagctaaacattttcgtggtcggtgattgatatcatataaagccttggttcccaaagcttttttatgttataaactca Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 91 HP_score: -6.5 Tail_Score: -5.5208 Start: 92 End: 108 Full_Region: TTGATATCATATAAA GCCTTGG TTC CCAAAGC TTTTTTATGTTATAA ...........................................................................................GCCTTGGTTCCCAAAGC.................... Find igs database================================================ Query_seq: SSA_0229:SSA_0230|SSA_0229:SSA_0230:hypothetical protein:hypothetical protein:-><-:223774..223901 128 gtgcaacatttactcgaactcatcctctagagcttcactagcagttctgtaagctaaacattttcgtggtcggtgattgatatcatataaagccttggttcccaaagcttttttatgttataaactca Intra-Species Hit: Count: 1 Min: 1 Max: 128 Len: 128 Subject: NC_009009_SSA_0229_SSA_0230|hypothetical protein:hypothetical protein|POSITIVE:NEGATIVE|[223774,223901]|128 HSP 1 e-value: 6.0E-67 bit: 254.0 Len: 128 Query Start:1 Query End:128 Subject Strand: POSITIVE Subject Start: 1 Subject End: 128 gtgcaacatttactcgaactcatcctctagagcttcactagcagttctgtaagctaaacattttcgtggtcggtgattgatatcatataaagccttggttcccaaagcttttttatgttataaactca gtgcaacatttactcgaactcatcctctagagcttcactagcagttctgtaagctaaacattttcgtggtcggtgattgatatcatataaagccttggttcccaaagcttttttatgttataaactca Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUGCAACAUUUACUCGAACUCAUCCUCUAGAGCUUCACUAGCAGUUCUGUAAGCUAAACAUUUUCGUGGUCGGUGAUUGAUAUCAUAUAAAGCCUUGGUUCCCAAAGCUUUUUUAUGUUAUAAACUCA ......((.((((.(((..........(((((((.(....).))))))).........(((....))).))))))).))....((((.(((((.((((...)))).)))))..))))........... (-21.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGAGUUUAUAACAUAAAAAAGCUUUGGGAACCAAGGCUUUAUAUGAUAUCAAUCACCGACCACGAAAAUGUUUAGCUUACAGAACUGCUAGUGAAGCUCUAGAGGAUGAGUUCGAGUAAAUGUUGCAC ((((((...(((((...((((((((((...))))))))))...((((....))))............))))).))))))..(((((.((((.......))))......)))))..(((.....))).. (-25.30) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 307 49 1 177 122 NC_009009:SSA_2227|5end_Acetyl_transferase,_putative_2228261..2228491_NEGATIVE 304 70 21 190 134 NC_009009:SSA_1572|5end_hypothetical_protein_1575908..1576138_NEGATIVE 300 80 31 148 99 NC_009009:SSA_1584|5end_Ring-cleavage_extradiol_dioxygenase,_putative_1587030..1587260_NEGATIVE 296 109 61 176 102 NC_009009:SSA_1897|5end_Ribosomal_protein_HS6-type_(S12/L30/L7a),_putative_1894450..1894680_NEGATIVE 291 56 12 230 186 NC_009009:SSA_1856|5end_hypothetical_protein_1852208..1852438_NEGATIVE 289 55 13 75 26 NC_009009:SSA_0973|5end_hypothetical_protein_980296..980526_POSITIVE 287 109 65 64 19 NC_009009:SSA_1180|5end_hypothetical_protein_1208559..1208789_NEGATIVE 285 55 14 122 76 NC_009009:SSA_0188|5end_hypothetical_protein_190798..191028_POSITIVE 283 57 18 67 7 NC_009009:SSA_1003|5end_ABC_transporter_substrate-binding_protein-multiple_sugars,_putative_1003875..1004105_POSITIVE 278 73 32 97 67 NC_009009:SSA_0538|5end_PduH_protein,_putative_533794..534024_POSITIVE 273 78 37 74 33 NC_009009:SSA_1577|5end_Proline_dipeptidase,_putative_1580294..1580524_POSITIVE 271 72 31 214 176 NC_009009:SSA_2010|5end_ABC-type_multidrug_transport_system,_permease_component,_putative_2012024..2012254_NEGATIVE 270 56 19 51 20 NC_009009:SSA_0996|5end_cGMP-specific_phosphodiesterase,_putative_996282..996512_POSITIVE 270 110 64 225 175 NC_009009:SSA_0088|5end_V-type_sodium_ATPase,_subunit_C,_putative_88930..89160_POSITIVE 268 60 13 72 20 NC_009009:SSA_0900|5end_Tetratricopeptide_repeat_(TPR)_family_protein_891068..891298_POSITIVE 266 66 21 53 10 NC_009009:SSA_1882|5end_Subtilisin-like_serine_proteases,_putative_1880797..1881027_NEGATIVE 262 55 15 157 100 NC_009009:SSA_2017|5end_Hypothetical_protein_(possibly_membrane-associated)_2017331..2017561_NEGATIVE 262 80 31 70 10 NC_009009:SSA_1070|5end_Ribosomal_large_subunit_pseudouridine_synthase_D,_putative_1088742..1088972_POSITIVE 262 66 24 231 198 NC_009009:SSA_0978|5end_hypothetical_protein_983736..983966_POSITIVE 261 76 31 137 68 NC_009009:SSA_1257|5end_hypothetical_protein_1283867..1284097_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 354 79 33 151 106 NC_009009:SSA_0406|3end_hypothetical_protein_402196..402346_NEGATIVE 310 108 62 147 97 NC_009009:SSA_2346|3end_3-oxoacyl-[acyl-carrier-protein]_synthase_III,_putative_2347602..2347752_NEGATIVE 289 55 13 63 14 NC_009009:SSA_0972|3end_hypothetical_protein_980364..980514_POSITIVE 286 40 1 151 112 NC_009009:SSA_2228|3end_Acetyltransferase_(GNAT)_family,_putative_2228271..2228421_NEGATIVE 286 67 37 149 115 NC_009009:SSA_0561|3end_RNA:NAD_2'-phosphotransferase,_putative_554255..554405_POSITIVE 285 55 14 96 50 NC_009009:SSA_0187|3end_Competence_protein_ComYD,_putative_190852..191002_POSITIVE 279 78 32 84 25 NC_009009:SSA_1710|3end_Transcriptional_regulator,_XRE_family,_putative_1699011..1699161_POSITIVE 278 73 32 116 86 NC_009009:SSA_0537|3end_Propanediol_utilization:dioldehydratase_reactivation,_putative_533893..534043_POSITIVE 271 46 7 122 83 NC_009009:SSA_0419|3end_Alpha-galactosidase,_putative_418530..418680_POSITIVE 270 71 31 82 20 NC_009009:SSA_1002|3end_Alpha-galactosidase,_putative_1003942..1004092_POSITIVE 268 60 13 85 33 NC_009009:SSA_0899|3end_Conserved_permease,_putative_891161..891311_POSITIVE 267 70 22 134 94 NC_009009:SSA_2022|3end_Transcriptional_regulator,_MerR_family_(multidrug-efflux_transporter_genes),_putative_2024488..2024638_POSITIVE 262 80 31 86 26 NC_009009:SSA_1069|3end_Lipoprotein_signal_peptidase,_putative_1088838..1088988_POSITIVE 261 76 31 146 77 NC_009009:SSA_1258|3end_Purine_nucleoside_phosphorylase,_family_1,_putative_1283858..1284008_NEGATIVE 261 78 31 147 100 NC_009009:SSA_0989|3end_Conserved_protein,_possible_transcriptional_regulator_(sigma-70,_region_4),_putative_991816..991966_POSITIVE 250 109 63 98 54 NC_009009:SSA_0494|3end_ABC-type_dipeptide/oligopeptide/nickel_transport_system,_ATPase_component,_putative_495269..495419_POSITIVE 250 69 22 145 93 NC_009009:SSA_0065|3end_Low_molecular_weight_phosphotyrosine_protein_phosphatase,_putative_67677..67827_POSITIVE 249 77 31 44 7 NC_009009:SSA_1573|3end_hypothetical_protein_1576054..1576204_NEGATIVE 248 77 31 141 100 NC_009009:SSA_0908|3end_ABC-type_uncharacterized_transport_system,_periplasmic_component,_putative_920787..920937_POSITIVE 241 85 41 139 85 NC_009009:SSA_2119|3end_Pentose-5-phosphate-3-epimerase,_putative_2120439..2120589_NEGATIVE