Origin IGS: taattgttaataaacaatgaatatccagcaaataagaaatgcaacgataatcgttgaatatgggggaaagaaaattctgatcgaccccatgttgggaaagaaaggctgc .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gcagcctttctttcccaacatggggtcgatcagaattttctttcccccatattcaacgattatcgttgcatttcttatttgctggatattcattgtttattaacaatta Mask Tandem Repeat Region ================================================ taattgttaataaacaatgaatatccagcaaataagaaatgcaacgataatcgttgaatatgggggaaagaaaattctgatcgaccccatgttgggaaagaaaggctgc Find is-nt database================================================ Query_seq: PI0382:PI0383|PI0382:PI0383:conserved hypothetical protein:conserved hypothetical protein; possible Zn-dependent hydrolase:->->:352184..352292 109 taattgttaataaacaatgaatatccagcaaataagaaatgcaacgataatcgttgaatatgggggaaagaaaattctgatcgaccccatgttgggaaagaaaggctgc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI0382:PI0383|PI0382:PI0383:conserved hypothetical protein:conserved hypothetical protein; possible Zn-dependent hydrolase:->->:352184..352292 109 taattgttaataaacaatgaatatccagcaaataagaaatgcaacgataatcgttgaatatgggggaaagaaaattctgatcgaccccatgttgggaaagaaaggctgc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI0382:PI0383|PI0382:PI0383:conserved hypothetical protein:conserved hypothetical protein; possible Zn-dependent hydrolase:->->:352184..352292 109 taattgttaataaacaatgaatatccagcaaataagaaatgcaacgataatcgttgaatatgggggaaagaaaattctgatcgaccccatgttgggaaagaaaggctgc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taattgttaataaacaatgaatatccagcaaataagaaatgcaacgataatcgttgaatatgggggaaagaaaattctgatcgaccccatgttgggaaagaaaggctgc Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: + Start: 17 End: 109 ................ M N I Q Q I R N A T I I V E Y G G K K I L I D P M L G K K G C taattgttaataaacaatgaatatccagcaaataagaaatgcaacgataatcgttgaatatgggggaaagaaaattctgatcgaccccatgttgggaaagaaaggctgc 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================================================ taattgttaataaacaatgaatatccagcaaataagaaatgcaacgataatcgttgaatatgggggaaagaaaattctgatcgaccccatgttgggaaagaaaggctgc Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 73 HP_score: -6.0 Tail_Score: -4.60258 Start: 40 End: 58 Full_Region: tttctttcccccata ttcaacga tta tcgttgca tttcttatttgctgg .......................................ttcaacgattatcgttgca................................................... TransTerm Strand: - Conf: 70 HP_score: -8.6 Tail_Score: -2.59958 Start: 42 End: 56 Full_Region: tctttcccccatatt caacga tta tcgttg catttcttatttgct .........................................caacgattatcgttg..................................................... Find igs database================================================ Query_seq: PI0382:PI0383|PI0382:PI0383:conserved hypothetical protein:conserved hypothetical protein; possible Zn-dependent hydrolase:->->:352184..352292 109 taattgttaataaacaatgaatatccagcaaataagaaatgcaacgataatcgttgaatatgggggaaagaaaattctgatcgaccccatgttgggaaagaaaggctgc Intra-Species Hit: Count: 1 Min: 1 Max: 109 Len: 109 Subject: pint_PI0382_PI0383|conserved hypothetical protein:conserved hypothetical protein; possible Zn-dependent hydrolase|POSITIVE:POSITIVE|[352184,352292]|109 HSP 1 e-value: 1.0E-55 bit: 216.0 Len: 109 Query Start:1 Query End:109 Subject Strand: POSITIVE Subject Start: 1 Subject End: 109 taattgttaataaacaatgaatatccagcaaataagaaatgcaacgataatcgttgaatatgggggaaagaaaattctgatcgaccccatgttgggaaagaaaggctgc taattgttaataaacaatgaatatccagcaaataagaaatgcaacgataatcgttgaatatgggggaaagaaaattctgatcgaccccatgttgggaaagaaaggctgc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAUUGUUAAUAAACAAUGAAUAUCCAGCAAAUAAGAAAUGCAACGAUAAUCGUUGAAUAUGGGGGAAAGAAAAUUCUGAUCGACCCCAUGUUGGGAAAGAAAGGCUGC ..((((((....)))))).......((((............(((((.....)))))(((((((((...(((....)))......)))))))))...........)))). (-25.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GCAGCCUUUCUUUCCCAACAUGGGGUCGAUCAGAAUUUUCUUUCCCCCAUAUUCAACGAUUAUCGUUGCAUUUCUUAUUUGCUGGAUAUUCAUUGUUUAUUAACAAUUA .((((..............((((((..((..(((....))).))))))))...(((((.....)))))............)))).......((((((....)))))).. (-21.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 279 97 55 147 87 pint:PI1546|5end_mobilizable_transposon,_excision_protein_1464060..1464290_POSITIVE 264 89 41 222 168 pint:PI1128|5end_probable_yrdC_domain_protein,_translation_factor_(SUA5)_1054463..1054693_POSITIVE 259 99 61 43 15 pint:PI0965|5end_hypothetical_protein_894154..894384_POSITIVE 253 89 51 61 18 pint:PI1067|5end_thymidylate_synthase_983940..984170_POSITIVE 250 66 25 80 39 pint:PI1241|5end_probable_phosphoesterase_1166365..1166595_POSITIVE 248 95 51 153 108 pint:PI1547|5end_hypothetical_protein_1465808..1466038_POSITIVE 247 70 34 230 196 pint:PI0900|5end_signal_recognition_particle_protein_829663..829893_POSITIVE 243 96 60 37 4 pint:PI2152|5end_heptosyltransferase_2098218..2098448_POSITIVE 243 89 41 151 112 pint:PI0198|5end_hypothetical_protein_190719..190949_POSITIVE 241 65 24 170 122 pint:PI1099|5end_low_molecular_weight_protein-tyrosine-phosphatase_1023059..1023289_POSITIVE 238 89 53 38 2 pint:PI2169|5end_hypothetical_protein_2111706..2111936_POSITIVE 238 66 26 224 181 pint:PI1208|5end_monofunctional_biosynthetic_peptidoglycan_transglycosylase_1127155..1127385_POSITIVE 238 66 26 116 73 pint:PI1205|5end_hypothetical_protein_1127047..1127277_POSITIVE 238 66 26 46 3 pint:PI1207|5end_hypothtical_protein_1126977..1127207_POSITIVE 229 72 35 64 23 pint:PI1457|5end_N-acetylmuramoyl-L-alanine_amidase_1379850..1380080_POSITIVE 228 97 51 136 100 pint:PI0345|5end_conserved_hypothetical_protein_319485..319715_POSITIVE 225 95 52 231 189 pint:PI1856|5end_nicotinate-nucleotide_adenylyltransferase_1803203..1803433_POSITIVE 225 88 43 184 145 pint:PI0170|5end_hypothetical_protein_163305..163535_POSITIVE 225 88 43 43 4 pint:PI0167|5end_hypothetical_protein_163164..163394_POSITIVE 223 66 24 86 34 pint:PI1833|5end_bacterioferritin_comigratory_protein_1773957..1774187_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 279 97 55 141 81 pint:PI1545|3end_conserved_hypothetical_protein_1464134..1464284_POSITIVE 278 97 52 100 51 pint:PI0780|3end_DNA_gyrase,_subunit_A_(DNA_topoisomerase_(ATP-hydrolyzing))_718513..718663_POSITIVE 257 66 22 104 51 pint:PI1726|3end_ATP-dependent_DNA_helicase_1645542..1645692_POSITIVE 242 89 41 143 92 pint:PI2167|3end_hypothetical_protein_2111891..2112041_POSITIVE 238 89 44 115 58 pint:PI1883|3end_conserved_hypothetical_protein;_possible_surface_protein_1826174..1826324_POSITIVE 238 66 26 121 78 pint:PI1206|3end_ATP-dependent_DNA_helicase,_UvrD/PcrA/Rep_family_1127132..1127282_POSITIVE 229 98 55 127 92 pint:PI1833|3end_bacterioferritin_comigratory_protein_1774495..1774645_POSITIVE 229 72 35 55 14 pint:PI1456|3end_conserved_hypothetical_protein_1379921..1380071_POSITIVE 225 95 52 116 74 pint:PI1855|3end_lipopolysaccharide_biosynthesis_protein_1803168..1803318_POSITIVE 225 88 43 78 39 pint:PI0168|3end_methionyl-tRNA_synthetase_(methionine--tRNA_ligase)_163279..163429_POSITIVE 223 66 24 72 20 pint:PI1832|3end_conserved_hypothetical_protein_1774023..1774173_POSITIVE 221 86 43 66 10 pint:PI1045|3end_cytidine/deoxycytidylate_deaminase_family_protein_965648..965798_POSITIVE 219 99 53 88 16 pint:PI0287|3end_ISPg3-related_transposase_272352..272502_POSITIVE 217 97 55 72 8 pint:PI0256|3end_conjugative_transposon_protein,_TraE_249420..249570_POSITIVE 216 56 15 141 89 pint:PI0105|3end_possible_sulfatase_101453..101603_POSITIVE 215 88 46 51 8 pint:PI0282|3end_hypothetical_protein_266826..266976_POSITIVE 214 54 24 140 106 pint:PI1098|3end_conserved_hypothetical_protein_1023123..1023273_POSITIVE 214 43 13 67 30 pint:PI0100|3end_LPS_biosynthesis_protein_(lipopolysaccharide_biosynthesis_protein)_96726..96876_POSITIVE 213 68 21 130 67 pint:PI1898|3end_S-adenosyl-methyltransferase_1842444..1842594_POSITIVE 211 93 60 34 1 pint:PI0382|3end_conserved_hypothetical_protein_352123..352273_POSITIVE