Origin IGS: agggcgtagttgttatgctgtgaaataagggaaatgtacggttcgttattggggaatgaagcgtataaggataagcttgtgtaagtgttttagtacaaaaagcgggtgtgtcaagttctgtttttgacacacccgcttgttttatttcgtttctta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 taagaaacgaaataaaacaagcgggtgtgtcaaaaacagaacttgacacacccgctttttgtactaaaacacttacacaagcttatccttatacgcttcattccccaataacgaaccgtacatttcccttatttcacagcataacaactacgccct Mask Tandem Repeat Region ================================================ agggcgtagttgttatgctgtgaaataagggaaatgtacggttcgttattggggaatgaagcgtataaggataagcttgtgtaagtgttttagtacaaaaagcgggtgtgtcaagttctgtttttgacacacccgcttgttttatttcgtttctta Find is-nt database================================================ Query_seq: PI2039:PI2040|PI2039:PI2040:hypothetical protein:conserved hypothetical protein; possible transporter:->->:1993052..1993207 156 agggcgtagttgttatgctgtgaaataagggaaatgtacggttcgttattggggaatgaagcgtataaggataagcttgtgtaagtgttttagtacaaaaagcgggtgtgtcaagttctgtttttgacacacccgcttgttttatttcgtttctta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI2039:PI2040|PI2039:PI2040:hypothetical protein:conserved hypothetical protein; possible transporter:->->:1993052..1993207 156 agggcgtagttgttatgctgtgaaataagggaaatgtacggttcgttattggggaatgaagcgtataaggataagcttgtgtaagtgttttagtacaaaaagcgggtgtgtcaagttctgtttttgacacacccgcttgttttatttcgtttctta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI2039:PI2040|PI2039:PI2040:hypothetical protein:conserved hypothetical protein; possible transporter:->->:1993052..1993207 156 agggcgtagttgttatgctgtgaaataagggaaatgtacggttcgttattggggaatgaagcgtataaggataagcttgtgtaagtgttttagtacaaaaagcgggtgtgtcaagttctgtttttgacacacccgcttgttttatttcgtttctta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 agggcgtagttgttatgctgtgaaataagggaaatgtacggttcgttattggggaatgaagcgtataaggataagcttgtgtaagtgttttagtacaaaaagcgggtgtgtcaagttctgtttttgacacacccgcttgttttatttcgtttctta Predict ORF larger than 30AA ================================================ Protein_Len: 48 Strand: - Start: 2 End: 145 . P T T T I S H F L P F T R N T I P S H L T Y P Y A Q T L T K T C F A P T D L E T K S V G A Q K M ........... agggcgtagttgttatgctgtgaaataagggaaatgtacggttcgttattggggaatgaagcgtataaggataagcttgtgtaagtgttttagtacaaaaagcgggtgtgtcaagttctgtttttgacacacccgcttgttttatttcgtttctta 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================================================ agggcgtagttgttatgctgtgaaataagggaaatgtacggttcgttattggggaatgaagcgtataaggataagcttgtgtaagtgttttagtacaaaaagcgggtgtgtcaagttctgtttttgacacacccgcttgttttatttcgtttctta Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 100 HP_score: -14.9 Tail_Score: -5.06223 Start: 99 End: 139 Full_Region: AGTGTTTTAGTACAA AAAGCGGGTGTGTCAAG TTCTGTT TTTGACACACCCGCTTG TTTTATTTCGTTTCT ..................................................................................................AAAGCGGGTGTGTCAAGTTCTGTTTTTGACACACCCGCTTG................. TransTerm Strand: + Conf: 100 HP_score: -16.6 Tail_Score: -4.57791 Start: 102 End: 136 Full_Region: GTTTTAGTACAAAAA GCGGGTGTGTCAAG TTCTGTT TTTGACACACCCGC TTGTTTTATTTCGTT .....................................................................................................GCGGGTGTGTCAAGTTCTGTTTTTGACACACCCGC.................... Find igs database================================================ Query_seq: PI2039:PI2040|PI2039:PI2040:hypothetical protein:conserved hypothetical protein; possible transporter:->->:1993052..1993207 156 agggcgtagttgttatgctgtgaaataagggaaatgtacggttcgttattggggaatgaagcgtataaggataagcttgtgtaagtgttttagtacaaaaagcgggtgtgtcaagttctgtttttgacacacccgcttgttttatttcgtttctta Intra-Species Hit: Count: 1 Min: 1 Max: 156 Len: 156 Subject: pint_PI2039_PI2040|hypothetical protein:conserved hypothetical protein; possible transporter|POSITIVE:POSITIVE|[1993052,1993207]|156 HSP 1 e-value: 1.0E-83 bit: 309.0 Len: 156 Query Start:1 Query End:156 Subject Strand: POSITIVE Subject Start: 1 Subject End: 156 agggcgtagttgttatgctgtgaaataagggaaatgtacggttcgttattggggaatgaagcgtataaggataagcttgtgtaagtgttttagtacaaaaagcgggtgtgtcaagttctgtttttgacacacccgcttgttttatttcgtttctta agggcgtagttgttatgctgtgaaataagggaaatgtacggttcgttattggggaatgaagcgtataaggataagcttgtgtaagtgttttagtacaaaaagcgggtgtgtcaagttctgtttttgacacacccgcttgttttatttcgtttctta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGGGCGUAGUUGUUAUGCUGUGAAAUAAGGGAAAUGUACGGUUCGUUAUUGGGGAAUGAAGCGUAUAAGGAUAAGCUUGUGUAAGUGUUUUAGUACAAAAAGCGGGUGUGUCAAGUUCUGUUUUUGACACACCCGCUUGUUUUAUUUCGUUUCUUA ..(((((((...)))))))..(((((((((....((((((.((((((.......)))))).)))))).........(((((..((....))..))))).((((((((((((((((.......)))))))))))))))).)))))))))........ (-50.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAGAAACGAAAUAAAACAAGCGGGUGUGUCAAAAACAGAACUUGACACACCCGCUUUUUGUACUAAAACACUUACACAAGCUUAUCCUUAUACGCUUCAUUCCCCAAUAACGAACCGUACAUUUCCCUUAUUUCACAGCAUAACAACUACGCCCU ........(((((((...(((((((((((((((.........)))))))))))))))..(((((..............((((.(((....))).))))..(((.........)))..)))))......)))))))..................... (-36.00) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 453 148 101 198 142 pint:PI0426|5end_conserved_hypothetical_protein_389345..389575_POSITIVE 386 138 100 158 120 pint:PI0313|5end_conserved_hypothetical_protein_294833..295063_POSITIVE 386 138 100 46 8 pint:PI0311|5end_hypothetical_protein_294721..294951_POSITIVE 307 149 101 216 165 pint:PI0284|5end_flavoprotein_A_268848..269078_POSITIVE 306 44 1 231 180 pint:PI1453|5end_probable_thiamine_pyrophosphokinase_1375982..1376212_POSITIVE 293 46 1 76 39 pint:PI1251|5end_hypothetical_protein_1174740..1174970_POSITIVE 290 47 4 209 162 pint:PI2094|5end_hypothetical_protein_2049540..2049770_POSITIVE 290 70 29 148 110 pint:PI1135|5end_hypothetical_protein_1061935..1062165_POSITIVE 285 138 91 157 102 pint:PI1086|5end_pyruvate:ferredoxin_oxidoreductase_1006602..1006832_POSITIVE 281 150 102 176 121 pint:PI0260|5end_conjugative_transposon_protein,_TraJ_253023..253253_POSITIVE 280 150 102 66 7 pint:PI0424|5end_methylated-DNA--[protein]-cysteine_S-methyltransferase_388429..388659_POSITIVE 279 150 101 156 114 pint:PI1463|5end_fumarate_hydratase,_class_I_1385349..1385579_POSITIVE 279 145 101 145 106 pint:PI1418|5end_UDP-N-acetylglucosamine_2-epimerase_1337985..1338215_POSITIVE 279 47 3 216 166 pint:PI0699|5end_conserved_hypothetical_protein_636647..636877_POSITIVE 266 87 49 61 22 pint:PI1672|5end_conserved_hypothetical_protein;_possible_DNA-binding_protein,_histone-like_family_1587027..1587257_POSITIVE 266 69 33 218 179 pint:PI1544|5end_hypothetical_protein_1463507..1463737_POSITIVE 266 136 95 135 99 pint:PI1124|5end_possible_nucleoside-diphosphate_sugar_epimerase_1049524..1049754_POSITIVE 265 150 101 196 159 pint:PI1940|5end_conserved_hypothetical_protein;_possible_outer_membrane_protein_1895730..1895960_POSITIVE 263 90 42 65 29 pint:PI1864|5end_chromate_transport_protein_1810318..1810548_POSITIVE 263 140 102 35 2 pint:PI0874|5end_conserved_hypothetical_protein_808978..809208_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 462 138 99 56 16 pint:PI0128|3end_dipeptidase,_pathogenicity_island-encoded_protein_D_121826..121976_POSITIVE 293 141 102 150 99 pint:PI2122|3end_conserved_hypothetical_protein_2070480..2070630_POSITIVE 292 120 78 151 94 pint:PI0129|3end_hypothetical_protein_121941..122091_POSITIVE 285 80 40 125 71 pint:PI1939|3end_hypothetical_protein_1896666..1896816_POSITIVE 284 147 101 127 84 pint:PI0173|3end_hypothetical_protein_165558..165708_POSITIVE 281 150 102 116 61 pint:PI0259|3end_conserved_protein_found_in_conjugation,_TraI_253043..253193_POSITIVE 279 150 101 110 68 pint:PI1462|3end_hypothetical_protein_1385383..1385533_POSITIVE 279 109 61 78 33 pint:PI1414|3end_conserved_hypothetical_protein_1334436..1334586_POSITIVE 274 130 84 140 90 pint:PI2001|3end_hypothetical_protein_1960478..1960628_POSITIVE 271 46 9 37 3 pint:PI1250|3end_RNA_polymerase_ECF-type_sigma_70_factor_1174781..1174931_POSITIVE 270 108 61 93 36 pint:PI0101|3end_lauroyl/myristoyl_acyltransferase_97753..97903_POSITIVE 269 133 103 151 123 pint:PI0869|3end_possible_exodeoxyribonuclease_VII_(small_subunit)_805774..805924_POSITIVE 266 79 40 115 73 pint:PI2008|3end__ABC_transporter,_ATP-binding_protein_1967961..1968111_POSITIVE 263 90 42 59 23 pint:PI1863|3end_phosphoribosylformylglycinamidine_synthase_1810392..1810542_POSITIVE 262 88 42 149 103 pint:PI1398|3end_probable_imidazolonepropionase_1320672..1320822_POSITIVE 261 149 101 130 80 pint:PI0073|3end_dihydropteroate_synthase_71785..71935_POSITIVE 260 42 3 99 53 pint:PI1949|3end_aminotransferase,_class_V_1904530..1904680_POSITIVE 258 150 101 71 29 pint:PI2104|3end_carboxyl-terminal_protease_2059390..2059540_POSITIVE 258 79 36 61 5 pint:PI1236|3end_10_kDa_chaperonin,_cpn10,_GroES_1159280..1159430_POSITIVE 257 135 91 51 13 pint:PI2108|3end_cell_surface_protein;_possible_cell_surface_antigen_BspA_2060625..2060775_POSITIVE