Origin IGS: taataaaagcattgtttcaacaacaatcaaccgttttttcaaacgcgtgcgtcagactattctttggcgcacgcgcttttctttttctgcacacatagaattctcttccttatctttgtta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 taacaaagataaggaagagaattctatgtgtgcagaaaaagaaaagcgcgtgcgccaaagaatagtctgacgcacgcgtttgaaaaaacggttgattgttgttgaaacaatgcttttatta Mask Tandem Repeat Region ================================================ taataaaagcattgtttcaacaacaatcaaccgttttttcaaacgcgtgcgtcagactattctttggcgcacgcgcttttctttttctgcacacatagaattctcttccttatctttgtta Find is-nt database================================================ Query_seq: PI2038:PI2039|PI2038:PI2039:conserved hypothetical protein; possible internalin-related protein:hypothetical protein:->->:1992652..1992772 121 taataaaagcattgtttcaacaacaatcaaccgttttttcaaacgcgtgcgtcagactattctttggcgcacgcgcttttctttttctgcacacatagaattctcttccttatctttgtta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI2038:PI2039|PI2038:PI2039:conserved hypothetical protein; possible internalin-related protein:hypothetical protein:->->:1992652..1992772 121 taataaaagcattgtttcaacaacaatcaaccgttttttcaaacgcgtgcgtcagactattctttggcgcacgcgcttttctttttctgcacacatagaattctcttccttatctttgtta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI2038:PI2039|PI2038:PI2039:conserved hypothetical protein; possible internalin-related protein:hypothetical protein:->->:1992652..1992772 121 taataaaagcattgtttcaacaacaatcaaccgttttttcaaacgcgtgcgtcagactattctttggcgcacgcgcttttctttttctgcacacatagaattctcttccttatctttgtta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taataaaagcattgtttcaacaacaatcaaccgttttttcaaacgcgtgcgtcagactattctttggcgcacgcgcttttctttttctgcacacatagaattctcttccttatctttgtta Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: + Start: 3 End: 95 .. M K A L F Q Q Q S T V F S N A C V R L F F G A R A F L F L H T .......................... Protein_Len: 37 Strand: + Start: 11 End: 121 .......... M V S T T I N R F F K R V R Q T I L W R T R F S F S A H I E F S S L S L L taataaaagcattgtttcaacaacaatcaaccgttttttcaaacgcgtgcgtcagactattctttggcgcacgcgcttttctttttctgcacacatagaattctcttccttatctttgtta 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================================================ taataaaagcattgtttcaacaacaatcaaccgttttttcaaacgcgtgcgtcagactattctttggcgcacgcgcttttctttttctgcacacatagaattctcttccttatctttgtta Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 100 HP_score: -11.0 Tail_Score: -5.35224 Start: 43 End: 76 Full_Region: CAACCGTTTTTTCAA ACGCGTGCGTCAGA CTATTC TTTGGCGCACGCGC TTTTCTTTTTCTGCA ..........................................ACGCGTGCGTCAGACTATTCTTTGGCGCACGCGC............................................. TransTerm Strand: + Conf: 100 HP_score: -14.5 Tail_Score: -3.79508 Start: 44 End: 75 Full_Region: AACCGTTTTTTCAAA CGCGTGCGTCAGA CTATTC TTTGGCGCACGCG CTTTTCTTTTTCTGC ...........................................CGCGTGCGTCAGACTATTCTTTGGCGCACGCG.............................................. TransTerm Strand: - Conf: 79 HP_score: -10.1 Tail_Score: -3.53343 Start: 44 End: 75 Full_Region: gcagaaaaagaaaag cgcgtgcgccaaa gaatag tctgacgcacgcg tttgaaaaaacggtt ...........................................cgcgtgcgccaaagaatagtctgacgcacgcg.............................................. Find igs database================================================ Query_seq: PI2038:PI2039|PI2038:PI2039:conserved hypothetical protein; possible internalin-related protein:hypothetical protein:->->:1992652..1992772 121 taataaaagcattgtttcaacaacaatcaaccgttttttcaaacgcgtgcgtcagactattctttggcgcacgcgcttttctttttctgcacacatagaattctcttccttatctttgtta Intra-Species Hit: Count: 1 Min: 1 Max: 121 Len: 121 Subject: pint_PI2038_PI2039|conserved hypothetical protein; possible internalin-related protein:hypothetical protein|POSITIVE:POSITIVE|[1992652,1992772]|121 HSP 1 e-value: 8.0E-63 bit: 240.0 Len: 121 Query Start:1 Query End:121 Subject Strand: POSITIVE Subject Start: 1 Subject End: 121 taataaaagcattgtttcaacaacaatcaaccgttttttcaaacgcgtgcgtcagactattctttggcgcacgcgcttttctttttctgcacacatagaattctcttccttatctttgtta taataaaagcattgtttcaacaacaatcaaccgttttttcaaacgcgtgcgtcagactattctttggcgcacgcgcttttctttttctgcacacatagaattctcttccttatctttgtta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAUAAAAGCAUUGUUUCAACAACAAUCAACCGUUUUUUCAAACGCGUGCGUCAGACUAUUCUUUGGCGCACGCGCUUUUCUUUUUCUGCACACAUAGAAUUCUCUUCCUUAUCUUUGUUA (((((((.(.((((((.....)))))))...............(((((((((((((......))))))))))))).........(((((......)))))..............))))))) (-26.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAACAAAGAUAAGGAAGAGAAUUCUAUGUGUGCAGAAAAAGAAAAGCGCGUGCGCCAAAGAAUAGUCUGACGCACGCGUUUGAAAAAACGGUUGAUUGUUGUUGAAACAAUGCUUUUAUUA ......(.(((.((((.....)))).))).).....(((((..(((((((((((....(((....)))..))))))))))).............((((((.....)))))).))))).... (-27.30) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 407 108 63 189 143 pint:PI0313|5end_conserved_hypothetical_protein_294833..295063_POSITIVE 407 108 63 77 31 pint:PI0311|5end_hypothetical_protein_294721..294951_POSITIVE 352 74 31 143 101 pint:PI0545|5end_sugar_kinase_496411..496641_POSITIVE 343 80 31 67 1 pint:PI0753|5end_hypothetical_protein_683391..683621_POSITIVE 327 110 61 69 14 pint:PI1637|5end_hypothetical_protein_1554500..1554730_POSITIVE 325 90 44 174 123 pint:PI0737|5end_hypothetical_protein_671182..671412_POSITIVE 320 110 65 230 180 pint:PI1902|5end_hypothetical_protein_1844931..1845161_POSITIVE 318 90 64 83 53 pint:PI2055|5end_hypothetical_protein_2012999..2013229_POSITIVE 317 87 44 188 144 pint:PI0426|5end_conserved_hypothetical_protein_389345..389575_POSITIVE 301 109 66 160 114 pint:PI0668|5end_peptidyl-prolyl_cis-trans_isomerase_SlyD,_FKBP-type_(peptidylprolyl_isomerase)_610216..610446_POSITIVE 301 109 66 57 11 pint:PI0667|5end_hypothetical_protein_610113..610343_POSITIVE 300 90 47 172 120 pint:PI0950|5end_50S_ribosomal_protein_L31_883327..883557_POSITIVE 300 76 31 204 149 pint:PI0333|5end_hypothetical_protein_313478..313708_POSITIVE 292 90 44 75 29 pint:PI1647|5end_hypothetical_protein_1561564..1561794_POSITIVE 289 88 46 47 1 pint:PI1513|5end_conserved_hypothetical_protein_1430152..1430382_POSITIVE 288 74 31 77 32 pint:PI1763|5end_two-component_system_sensor_histidine_kinase/response_regulator_1685877..1686107_POSITIVE 288 89 45 186 145 pint:PI0467|5end_50S_ribosomal_protein_L16_436471..436701_POSITIVE 286 84 46 166 114 pint:PI0529|5end_hypothetical_protein_483026..483256_POSITIVE 285 90 47 162 127 pint:PI2099|5end_D-alanyl-D-alanine_dipeptidase_2052409..2052639_POSITIVE 284 82 44 68 23 pint:PI1675|5end_TonB-dependent_outer_membrane_receptor_1588107..1588337_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 442 75 44 47 16 pint:PI2038|3end_conserved_hypothetical_protein;_possible_internalin-related_protein_1992591..1992741_POSITIVE 318 79 32 149 109 pint:PI2155|3end_hypothetical_protein_2101052..2101202_POSITIVE 318 90 64 80 50 pint:PI2054|3end_hypothetical_protein_2013076..2013226_POSITIVE 316 80 43 63 3 pint:PI0752|3end_conserved_hypothetical_protein_683467..683617_POSITIVE 288 70 22 142 90 pint:PI0837|3end_conserved_hypothetical_protein_772681..772831_POSITIVE 285 90 47 146 111 pint:PI2098|3end_hypothetical_protein_2052473..2052623_POSITIVE 285 76 32 126 74 pint:PI1493|3end_conserved_hypothetical_protein_1412818..1412968_POSITIVE 275 90 44 69 7 pint:PI0417|3end_hypothetical_protein_386730..386880_POSITIVE 275 90 44 72 19 pint:PI0187|3end_hypothetical_protein_178211..178361_POSITIVE 272 98 67 118 82 pint:PI1768|3end_conserved_hypothetical_protein_1696639..1696789_POSITIVE 271 89 41 61 22 pint:PI1652|3end_hypothetical_protein_1565235..1565385_POSITIVE 266 76 31 105 54 pint:PI0027|3end_aminopeptidase_C_31756..31906_POSITIVE 265 69 27 147 102 pint:PI1187|3end_conserved_hypothetical_protein_1107245..1107395_POSITIVE 264 96 61 142 101 pint:PI0420|3end_hypothetical_protein_386828..386978_POSITIVE 263 99 57 94 44 pint:PI0335|3end_hypothetical_protein_314420..314570_POSITIVE 262 56 13 150 107 pint:PI0686|3end_glycosyl_transferase,_group_2_family_protein_624249..624399_POSITIVE 261 89 47 116 64 pint:PI2145|3end_hypothetical_protein_2092649..2092799_POSITIVE 259 90 41 140 94 pint:PI1644|3end_hypothetical_protein_1561030..1561180_POSITIVE 258 76 32 147 88 pint:PI2122|3end_conserved_hypothetical_protein_2070480..2070630_POSITIVE 258 75 36 49 3 pint:PI1647|3end_hypothetical_protein_1562531..1562681_POSITIVE