Origin IGS: ttcttgttttaaatcgttagaagtatgcaaatatagtccatttccttaaaactcccatcattttgcttaaaagttaggatatttttacgttcggttcattcagacagggctattcggagaacagctatgccaactgtaaacaaatcttaatacaaaagaaattgcagcaccaaatgtta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 taacatttggtgctgcaatttcttttgtattaagatttgtttacagttggcatagctgttctccgaatagccctgtctgaatgaaccgaacgtaaaaatatcctaacttttaagcaaaatgatgggagttttaaggaaatggactatatttgcatacttctaacgatttaaaacaagaa Mask Tandem Repeat Region ================================================ ttcttgttttaaatcgttagaagtatgcaaatatagtccatttccttaaaactcccatcattttgcttaaaagttaggatatttttacgttcggttcattcagacagggctattcggagaacagctatgccaactgtaaacaaatcttaatacaaaagaaattgcagcaccaaatgtta Find is-nt database================================================ Query_seq: PI1859:PI1861|PI1859:PI1861:conserved hypothetical protein:hypothetical protein:->->:1805888..1806066 179 ttcttgttttaaatcgttagaagtatgcaaatatagtccatttccttaaaactcccatcattttgcttaaaagttaggatatttttacgttcggttcattcagacagggctattcggagaacagctatgccaactgtaaacaaatcttaatacaaaagaaattgcagcaccaaatgtta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI1859:PI1861|PI1859:PI1861:conserved hypothetical protein:hypothetical protein:->->:1805888..1806066 179 ttcttgttttaaatcgttagaagtatgcaaatatagtccatttccttaaaactcccatcattttgcttaaaagttaggatatttttacgttcggttcattcagacagggctattcggagaacagctatgccaactgtaaacaaatcttaatacaaaagaaattgcagcaccaaatgtta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI1859:PI1861|PI1859:PI1861:conserved hypothetical protein:hypothetical protein:->->:1805888..1806066 179 ttcttgttttaaatcgttagaagtatgcaaatatagtccatttccttaaaactcccatcattttgcttaaaagttaggatatttttacgttcggttcattcagacagggctattcggagaacagctatgccaactgtaaacaaatcttaatacaaaagaaattgcagcaccaaatgtta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttcttgttttaaatcgttagaagtatgcaaatatagtccatttccttaaaactcccatcattttgcttaaaagttaggatatttttacgttcggttcattcagacagggctattcggagaacagctatgccaactgtaaacaaatcttaatacaaaagaaattgcagcaccaaatgtta Predict ORF larger than 30AA ================================================ Protein_Len: 36 Strand: + Start: 40 End: 147 ....................................... M S L K L P S F C L K V R I F L R S V H S D R A I R R T A M P T V N K S ................................ Protein_Len: 33 Strand: + Start: 81 End: 179 ................................................................................ M F T F G S F R Q G Y S E N S Y A N C K Q I L I Q K K L Q H Q M L ttcttgttttaaatcgttagaagtatgcaaatatagtccatttccttaaaactcccatcattttgcttaaaagttaggatatttttacgttcggttcattcagacagggctattcggagaacagctatgccaactgtaaacaaatcttaatacaaaagaaattgcagcaccaaatgtta 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================================================ ttcttgttttaaatcgttagaagtatgcaaatatagtccatttccttaaaactcccatcattttgcttaaaagttaggatatttttacgttcggttcattcagacagggctattcggagaacagctatgccaactgtaaacaaatcttaatacaaaagaaattgcagcaccaaatgtta Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PI1859:PI1861|PI1859:PI1861:conserved hypothetical protein:hypothetical protein:->->:1805888..1806066 179 ttcttgttttaaatcgttagaagtatgcaaatatagtccatttccttaaaactcccatcattttgcttaaaagttaggatatttttacgttcggttcattcagacagggctattcggagaacagctatgccaactgtaaacaaatcttaatacaaaagaaattgcagcaccaaatgtta Intra-Species Hit: Count: 1 Min: 1 Max: 179 Len: 179 Subject: pint_PI1859_PI1861|conserved hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[1805888,1806066]|179 HSP 1 e-value: 3.0E-97 bit: 355.0 Len: 179 Query Start:1 Query End:179 Subject Strand: POSITIVE Subject Start: 1 Subject End: 179 ttcttgttttaaatcgttagaagtatgcaaatatagtccatttccttaaaactcccatcattttgcttaaaagttaggatatttttacgttcggttcattcagacagggctattcggagaacagctatgccaactgtaaacaaatcttaatacaaaagaaattgcagcaccaaatgtta ttcttgttttaaatcgttagaagtatgcaaatatagtccatttccttaaaactcccatcattttgcttaaaagttaggatatttttacgttcggttcattcagacagggctattcggagaacagctatgccaactgtaaacaaatcttaatacaaaagaaattgcagcaccaaatgtta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUCUUGUUUUAAAUCGUUAGAAGUAUGCAAAUAUAGUCCAUUUCCUUAAAACUCCCAUCAUUUUGCUUAAAAGUUAGGAUAUUUUUACGUUCGGUUCAUUCAGACAGGGCUAUUCGGAGAACAGCUAUGCCAACUGUAAACAAAUCUUAAUACAAAAGAAAUUGCAGCACCAAAUGUUA .....(((((((.......((.((((....))))..)).......)))))))......(((((((((.....((((((((.(.((((((((.(((............((((.(((...))).))))..)))))).))))).).))))))))....((....))..))))..)))))... (-23.38) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAACAUUUGGUGCUGCAAUUUCUUUUGUAUUAAGAUUUGUUUACAGUUGGCAUAGCUGUUCUCCGAAUAGCCCUGUCUGAAUGAACCGAACGUAAAAAUAUCCUAACUUUUAAGCAAAAUGAUGGGAGUUUUAAGGAAAUGGACUAUAUUUGCAUACUUCUAACGAUUUAAAACAAGAA ..((.((((((...((((..((((.......)))).))))...((...((((..(((((((...)))))))..))))....)).)))))).)).......(((((.(((((....)))).).)))))((((((.(.(((((.....))))).).....((....))..))))))..... (-30.70) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 295 141 102 218 183 pint:PI0843|5end_carboxyl-terminal_protease_776145..776375_POSITIVE 292 137 94 218 166 pint:PI0030|5end_transcriptional_regulator,_AsnC_family_34509..34739_POSITIVE 281 137 92 174 127 pint:PI0409|5end_3-deoxy-D-manno-octulosonic-acid_transferase_(kdotransferase)_374648..374878_POSITIVE 279 140 101 206 170 pint:PI0130|5end_hypothetical_protein_122032..122262_POSITIVE 276 146 101 205 152 pint:PI1572|5end_hypothetical_protein_1497782..1498012_POSITIVE 275 140 93 83 35 pint:PI1429|5end_L-aspartate_oxidase_1347650..1347880_POSITIVE 273 150 105 116 68 pint:PI1530|5end_conserved_hypothetical_protein_1450439..1450669_POSITIVE 266 117 72 78 34 pint:PI2021|5end_DNA_repair_protein_1977925..1978155_POSITIVE 266 131 92 164 115 pint:PI1543|5end_hypothetical_protein_1462773..1463003_POSITIVE 266 137 92 87 46 pint:PI0751|5end_conserved_hypothetical_protein_680623..680853_POSITIVE 265 137 93 188 126 pint:PI1981|5end_hypothetical_protein_1937897..1938127_POSITIVE 263 140 102 95 49 pint:PI1858|5end_conserved_hypothetical_protein_1804400..1804630_POSITIVE 263 139 92 81 32 pint:PI1476|5end_acyl-CoA_synthase/O-succinylbenzoic_acid-CoA_ligase_1397699..1397929_POSITIVE 263 131 98 49 18 pint:PI0180|5end_TonB_protein_171905..172135_POSITIVE 262 148 104 107 57 pint:PI0736|5end_transcriptional_regulator,_TetR_family_670580..670810_POSITIVE 258 138 101 186 138 pint:PI2176|5end_conserved_hypothetical_protein_2116484..2116714_POSITIVE 258 135 98 217 161 pint:PI1896|5end_hypothetical_protein_1840854..1841084_POSITIVE 258 132 92 58 9 pint:PI1309|5end_excinuclease_ABC,_A_subunit_1223751..1223981_POSITIVE 258 139 92 205 156 pint:PI0733|5end_membrane_protein;_predicted_exporter_664389..664619_POSITIVE 257 139 92 60 1 pint:PI0680|5end_hypothetical_protein_616958..617188_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 281 130 81 64 13 pint:PI0326|3end_ISPg3-related_transposase_307768..307918_POSITIVE 276 130 87 113 61 pint:PI0060|3end_long-chain-fatty-acid--CoA_ligase_(acyl-CoA_synthetase)_60166..60316_POSITIVE 269 130 91 104 71 pint:PI0110|3end_ABC_transport_system,_ATP-binding_protein_107920..108070_POSITIVE 258 138 101 148 100 pint:PI2175|3end_RNA_polymerase_sigma-54_2116526..2116676_POSITIVE 258 59 14 117 68 pint:PI1979|3end_conserved_hypothetical_protein_1937327..1937477_POSITIVE 258 139 92 103 54 pint:PI0732|3end_conserved_hypothetical_protein_664367..664517_POSITIVE 256 140 98 104 63 pint:PI0168|3end_methionyl-tRNA_synthetase_(methionine--tRNA_ligase)_163279..163429_POSITIVE 255 147 104 73 12 pint:PI0738|3end_conserved_hypothetical_protein_671871..672021_POSITIVE 255 143 103 138 93 pint:PI0682|3end_hypothetical_protein_619372..619522_POSITIVE 243 136 91 145 96 pint:PI0177|3end_2-oxoglutarate_synthase,_subunit_korB_169583..169733_POSITIVE 242 140 94 48 1 pint:PI1428|3end_quinolinate_synthetase_A_1347695..1347845_POSITIVE 238 143 101 107 56 pint:PI2069|3end_ISPg3-related_transposase,_C-terminal_fragment_2029340..2029490_POSITIVE 237 69 21 136 91 pint:PI0207|3end_conserved_hypothetical_protein_200752..200902_POSITIVE 236 132 92 133 77 pint:PI0797|3end_tRNA_pseudouridine_synthase_A_(pseudouridylate_synthase)_735752..735902_POSITIVE 234 117 86 136 102 pint:PI0914|3end_ATPase,_AAA_family_844992..845142_POSITIVE 234 131 91 147 115 pint:PI0088|3end_S-adenosylmethionine_synthetase_88032..88182_POSITIVE 233 131 92 144 110 pint:PI0430|3end_periplasmic_protease;_MdsD_protein_403101..403251_POSITIVE 233 140 103 35 1 pint:PI0129|3end_hypothetical_protein_121941..122091_POSITIVE 232 140 99 147 98 pint:PI1761|3end_hypothetical_protein_1684543..1684693_POSITIVE 232 137 105 140 96 pint:PI1606|3end_conserved_hypothetical_protein_1535565..1535715_POSITIVE