Origin IGS: tttgttttatttatctattaattatacttaatcttgttatctcattataacggactgcaaagatactcattttcagataaatagagaaatgtttttcgctttttttgcaaaaactctttcataagctgtctgacaatctactttttttgtatctttgccccgtaatta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 taattacggggcaaagatacaaaaaaagtagattgtcagacagcttatgaaagagtttttgcaaaaaaagcgaaaaacatttctctatttatctgaaaatgagtatctttgcagtccgttataatgagataacaagattaagtataattaatagataaataaaacaaa Mask Tandem Repeat Region ================================================ tttgttttatttatctattaattatacttaatcttgttatctcattataacggactgcaaagatactcattttcagataaatagagaaatgtttttcgctttttttgcaaaaactctttcataagctgtctgacaatctactttttttgtatctttgccccgtaatta Find is-nt database================================================ Query_seq: PI0942:PI0944|PI0942:PI0944:DNA-binding protein HU:hypothetical protein:->->:875040..875207 168 tttgttttatttatctattaattatacttaatcttgttatctcattataacggactgcaaagatactcattttcagataaatagagaaatgtttttcgctttttttgcaaaaactctttcataagctgtctgacaatctactttttttgtatctttgccccgtaatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI0942:PI0944|PI0942:PI0944:DNA-binding protein HU:hypothetical protein:->->:875040..875207 168 tttgttttatttatctattaattatacttaatcttgttatctcattataacggactgcaaagatactcattttcagataaatagagaaatgtttttcgctttttttgcaaaaactctttcataagctgtctgacaatctactttttttgtatctttgccccgtaatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI0942:PI0944|PI0942:PI0944:DNA-binding protein HU:hypothetical protein:->->:875040..875207 168 tttgttttatttatctattaattatacttaatcttgttatctcattataacggactgcaaagatactcattttcagataaatagagaaatgtttttcgctttttttgcaaaaactctttcataagctgtctgacaatctactttttttgtatctttgccccgtaatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tttgttttatttatctattaattatacttaatcttgttatctcattataacggactgcaaagatactcattttcagataaatagagaaatgtttttcgctttttttgcaaaaactctttcataagctgtctgacaatctactttttttgtatctttgccccgtaatta Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: - Start: 48 End: 137 ............................................... L P S C L Y E N E S L Y L F T K R K K Q L F E K M L Q R V M ............................... tttgttttatttatctattaattatacttaatcttgttatctcattataacggactgcaaagatactcattttcagataaatagagaaatgtttttcgctttttttgcaaaaactctttcataagctgtctgacaatctactttttttgtatctttgccccgtaatta 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================================================ tttgttttatttatctattaattatacttaatcttgttatctcattataacggactgcaaagatactcattttcagataaatagagaaatgtttttcgctttttttgcaaaaactctttcataagctgtctgacaatctactttttttgtatctttgccccgtaatta Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PI0942:PI0944|PI0942:PI0944:DNA-binding protein HU:hypothetical protein:->->:875040..875207 168 tttgttttatttatctattaattatacttaatcttgttatctcattataacggactgcaaagatactcattttcagataaatagagaaatgtttttcgctttttttgcaaaaactctttcataagctgtctgacaatctactttttttgtatctttgccccgtaatta Intra-Species Hit: Count: 1 Min: 1 Max: 168 Len: 168 Subject: pint_PI0942_PI0944|DNA-binding protein HU:hypothetical protein|POSITIVE:POSITIVE|[875040,875207]|168 HSP 1 e-value: 1.0E-65 bit: 250.0 Len: 168 Query Start:1 Query End:168 Subject Strand: POSITIVE Subject Start: 1 Subject End: 168 tttgttttatttatctattaattatacttaatcttgttatctcattataacggactgcaaagatactcattttcagataaatagagaaatgtttttcgcnnnnnnngcaaaaactctttcataagctgtctgacaatctacnnnnnnngtatctttgccccgtaatta tttgttttatttatctattaattatacttaatcttgttatctcattataacggactgcaaagatactcattttcagataaatagagaaatgtttttcgctttttttgcaaaaactctttcataagctgtctgacaatctactttttttgtatctttgccccgtaatta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUGUUUUAUUUAUCUAUUAAUUAUACUUAAUCUUGUUAUCUCAUUAUAACGGACUGCAAAGAUACUCAUUUUCAGAUAAAUAGAGAAAUGUUUUUCGCUUUUUUUGCAAAAACUCUUUCAUAAGCUGUCUGACAAUCUACUUUUUUUGUAUCUUUGCCCCGUAAUUA ..................(((((((......(((.(((((......))))))))..((((((((((..(((.(((((((......((((.((((((.((.......))))))))..))))......))))))).)))...........))))))))))...))))))) (-30.02) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAUUACGGGGCAAAGAUACAAAAAAAGUAGAUUGUCAGACAGCUUAUGAAAGAGUUUUUGCAAAAAAAGCGAAAAACAUUUCUCUAUUUAUCUGAAAAUGAGUAUCUUUGCAGUCCGUUAUAAUGAGAUAACAAGAUUAAGUAUAAUUAAUAGAUAAAUAAAACAAA .....((((.((((((((((.....((.....)).(((((........((((...(((((((.......)))))))...))))........)))))......))))))))))...)))).................(((((......)))))................ (-30.89) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 256 75 31 113 68 pint:PI0572|5end_tRNA_(5-methylaminomethyl-2-thiouridylate)-methyltransferase_516382..516612_POSITIVE 244 149 115 197 164 pint:PI1262|5end_ISPg3-related_transposase,_C-terminal_region_1183967..1184197_POSITIVE 237 130 83 178 127 pint:PI0695|5end_xanthine/uracil_permease_family_protein_631413..631643_POSITIVE 227 98 56 148 95 pint:PI1689|5end_conserved_hypothetical_protein_1604310..1604540_POSITIVE 224 128 84 152 105 pint:PI1057|5end_hypothetical_protein_977286..977516_POSITIVE 224 160 113 85 41 pint:PI0580|5end_Holliday_junction_DNA_helicase_524178..524408_POSITIVE 222 72 32 93 48 pint:PI0538|5end_transcriptional_regulator_492561..492791_POSITIVE 220 108 61 205 144 pint:PI1253|5end_hypothetical_protein_1175516..1175746_POSITIVE 220 160 115 193 129 pint:PI1237|5end_ATP-dependent_DNA_helicase_1159688..1159918_POSITIVE 218 73 44 175 141 pint:PI1036|5end_ATP-dependent__Lon_protease_954446..954676_POSITIVE 218 130 89 209 162 pint:PI0265|5end_conjugative_transposon_protein,_TraO_257296..257526_POSITIVE 212 157 114 61 5 pint:PI0212|5end_surface_protein/internalin-related_protein_204417..204647_POSITIVE 211 118 71 169 118 pint:PI0202|5end_DNA_helicase_191753..191983_POSITIVE 206 131 93 160 124 pint:PI0261|5end_conjugative_transposon_protein,_TraK_254065..254295_POSITIVE 205 144 117 136 112 pint:PI2138|5end_nicotinate_phosphoribosyltransferase_2083836..2084066_POSITIVE 205 69 25 181 134 pint:PI1692|5end_alanine_racemase_1605691..1605921_POSITIVE 204 160 114 136 79 pint:PI1779|5end_16S_rRNA_processing_protein_1711335..1711565_POSITIVE 204 100 52 196 148 pint:PI1631|5end_hypothetical_protein_1552424..1552654_POSITIVE 203 132 96 221 199 pint:PI1492|5end_triosephosphate_isomerase_1410155..1410385_POSITIVE 203 132 91 225 181 pint:PI1205|5end_hypothetical_protein_1127047..1127277_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 267 160 119 148 110 pint:PI1370|3end_alkyl_hydroperoxide_reductase,_subunit_F_1292176..1292326_POSITIVE 256 75 31 100 55 pint:PI0571|3end_conserved_hypothetical_protein;_possible_permease_516449..516599_POSITIVE 238 143 101 96 56 pint:PI0434|3end_possible_beta-lactamase_406890..407040_POSITIVE 228 104 67 76 42 pint:PI0480|3end_preprotein_translocase,_SecY_subunit_442993..443143_POSITIVE 226 67 49 46 29 pint:PI0437|3end_conserved_hypothetical_protein;_possible_ribosomal_subunit_interface_protein_408543..408693_POSITIVE 222 72 32 75 30 pint:PI0536|3end_hypothetical_protein_492623..492773_POSITIVE 216 157 112 124 76 pint:PI1575|3end_LemA_protein_1501852..1502002_POSITIVE 213 158 111 68 21 pint:PI1610|3end_Na+/H+_anti-porter_1538002..1538152_POSITIVE 212 132 94 147 109 pint:PI2141|3end_hypothetical_protein_2087557..2087707_POSITIVE 212 74 33 140 95 pint:PI0238|3end_two-component_system_response_regulator_237826..237976_POSITIVE 211 139 107 54 18 pint:PI1734|3end_possible_carboxyl-terminal_protease-related_protein_1653829..1653979_POSITIVE 211 118 71 71 20 pint:PI0200|3end_hypothetical_protein_191735..191885_POSITIVE 206 160 113 150 90 pint:PI1550|3end_conserved_hypothetical_protein_1467703..1467853_POSITIVE 206 131 93 137 101 pint:PI0260|3end_conjugative_transposon_protein,_TraJ_254122..254272_POSITIVE 205 144 117 27 3 pint:PI2137|3end_RNA_methylase_SpoU_family_2083807..2083957_POSITIVE 205 69 25 146 99 pint:PI1691|3end_hypothetical_protein_1605736..1605886_POSITIVE 204 160 114 120 63 pint:PI1778|3end_UDP-N-acetylglucosamine_1-carboxyvinyltransferase_1711399..1711549_POSITIVE 201 130 90 146 113 pint:PI0750|3end_zinc_protease_680633..680783_POSITIVE 199 160 119 127 92 pint:PI1651|3end_hypothetical_protein_1564512..1564662_POSITIVE 198 158 113 149 99 pint:PI0763|3end_thymidine_kinase_698002..698152_POSITIVE