Origin IGS: aattgactgtttttaagttgatgattctgttcaaagggtacattcatgattgcatattggcaccattcgacaggttttcgtctcatatggttaaacagaatcggccggatttagttcccgatcgaatccgtccgatccgaaaactctgcgccccctgttgtatcttgggggaaatgaaaaagagcgaagaggaagggggaagctgaccattttttcttttcatgcgccgaaaaacaa .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ttgtttttcggcgcatgaaaagaaaaaatggtcagcttcccccttcctcttcgctctttttcatttcccccaagatacaacagggggcgcagagttttcggatcggacggattcgatcgggaactaaatccggccgattctgtttaaccatatgagacgaaaacctgtcgaatggtgccaatatgcaatcatgaatgtaccctttgaacagaatcatcaacttaaaaacagtcaatt Mask Tandem Repeat Region ================================================ aattgactgtttttaagttgatgattctgttcaaagggtacattcatgattgcatattggcaccattcgacaggttttcgtctcatatggttaaacagaatcggccggatttagttcccgatcgaatccgtccgatccgaaaactctgcgccccctgttgtatcttgggggaaatgaaaaagagcgaagaggaagggggaagctgaccattttttcttttcatgcgccgaaaaacaa Find is-nt database================================================ Query_seq: PG0421:PG0422|PG0421:PG0422:hypothetical protein:hypothetical protein:<-<-:461784..462020 237 aattgactgtttttaagttgatgattctgttcaaagggtacattcatgattgcatattggcaccattcgacaggttttcgtctcatatggttaaacagaatcggccggatttagttcccgatcgaatccgtccgatccgaaaactctgcgccccctgttgtatcttgggggaaatgaaaaagagcgaagaggaagggggaagctgaccattttttcttttcatgcgccgaaaaacaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG0421:PG0422|PG0421:PG0422:hypothetical protein:hypothetical protein:<-<-:461784..462020 237 aattgactgtttttaagttgatgattctgttcaaagggtacattcatgattgcatattggcaccattcgacaggttttcgtctcatatggttaaacagaatcggccggatttagttcccgatcgaatccgtccgatccgaaaactctgcgccccctgttgtatcttgggggaaatgaaaaagagcgaagaggaagggggaagctgaccattttttcttttcatgcgccgaaaaacaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG0421:PG0422|PG0421:PG0422:hypothetical protein:hypothetical protein:<-<-:461784..462020 237 aattgactgtttttaagttgatgattctgttcaaagggtacattcatgattgcatattggcaccattcgacaggttttcgtctcatatggttaaacagaatcggccggatttagttcccgatcgaatccgtccgatccgaaaactctgcgccccctgttgtatcttgggggaaatgaaaaagagcgaagaggaagggggaagctgaccattttttcttttcatgcgccgaaaaacaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aattgactgtttttaagttgatgattctgttcaaagggtacattcatgattgcatattggcaccattcgacaggttttcgtctcatatggttaaacagaatcggccggatttagttcccgatcgaatccgtccgatccgaaaactctgcgccccctgttgtatcttgggggaaatgaaaaagagcgaagaggaagggggaagctgaccattttttcttttcatgcgccgaaaaacaa Predict ORF larger than 30AA ================================================ Protein_Len: 60 Strand: + Start: 3 End: 203 .. M T V F K L M I L F K G Y I H D C I L A P F D R F S S H M V K Q N R P D L V P D R I R P I R K L C A P C C I L G E M K K .................................. Protein_Len: 30 Strand: + Start: 146 End: 235 ................................................................................................................................................. M R P L L Y L G G N E K E R R G R G K L T I F S F H A P K N .. Protein_Len: 39 Strand: - Start: 94 End: 210 ............................................................................................. V S D A P N L E R D F G D S G F V R R G R N Y R P P F S F S R L P L P F S V M ........................... Protein_Len: 46 Strand: - Start: 86 End: 223 ..................................................................................... I T L C F R G S K T G S R I R G I R F S Q A G Q Q I K P S I F F L S S S P P L Q G N K R K M .............. Protein_Len: 36 Strand: - Start: 3 End: 110 .. Q S N K L Q H N Q E F P V N M I A Y Q C W E V P K R R M H N F L I P R M ............................................................................................................................... aattgactgtttttaagttgatgattctgttcaaagggtacattcatgattgcatattggcaccattcgacaggttttcgtctcatatggttaaacagaatcggccggatttagttcccgatcgaatccgtccgatccgaaaactctgcgccccctgttgtatcttgggggaaatgaaaaagagcgaagaggaagggggaagctgaccattttttcttttcatgcgccgaaaaacaa 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================================================ aattgactgtttttaagttgatgattctgttcaaagggtacattcatgattgcatattggcaccattcgacaggttttcgtctcatatggttaaacagaatcggccggatttagttcccgatcgaatccgtccgatccgaaaactctgcgccccctgttgtatcttgggggaaatgaaaaagagcgaagaggaagggggaagctgaccattttttcttttcatgcgccgaaaaacaa Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 56 HP_score: -5.4 Tail_Score: -3.37487 Start: 98 End: 138 Full_Region: gggcgcagagttttc ggatcggacggattcgat cggga actaaatccggccgattc tgtttaaccatatga .................................................................................................ggatcggacggattcgatcgggaactaaatccggccgattc................................................................................................... TransTerm Strand: - Conf: 53 HP_score: -3.5 Tail_Score: -3.82202 Start: 101 End: 135 Full_Region: cgcagagttttcgga tcggacggattcgat cggga actaaatccggccga ttctgtttaaccata ....................................................................................................tcggacggattcgatcgggaactaaatccggccga...................................................................................................... Find igs database================================================ Query_seq: PG0421:PG0422|PG0421:PG0422:hypothetical protein:hypothetical protein:<-<-:461784..462020 237 aattgactgtttttaagttgatgattctgttcaaagggtacattcatgattgcatattggcaccattcgacaggttttcgtctcatatggttaaacagaatcggccggatttagttcccgatcgaatccgtccgatccgaaaactctgcgccccctgttgtatcttgggggaaatgaaaaagagcgaagaggaagggggaagctgaccattttttcttttcatgcgccgaaaaacaa Intra-Species Hit: Count: 1 Min: 1 Max: 237 Len: 237 Subject: NC_002950_PG0421_PG0422|hypothetical protein:hypothetical protein|NEGATIVE:NEGATIVE|[461784,462020]|237 HSP 1 e-value: 1.0E-131 bit: 470.0 Len: 237 Query Start:1 Query End:237 Subject Strand: POSITIVE Subject Start: 1 Subject End: 237 aattgactgtttttaagttgatgattctgttcaaagggtacattcatgattgcatattggcaccattcgacaggttttcgtctcatatggttaaacagaatcggccggatttagttcccgatcgaatccgtccgatccgaaaactctgcgccccctgttgtatcttgggggaaatgaaaaagagcgaagaggaagggggaagctgaccattttttcttttcatgcgccgaaaaacaa aattgactgtttttaagttgatgattctgttcaaagggtacattcatgattgcatattggcaccattcgacaggttttcgtctcatatggttaaacagaatcggccggatttagttcccgatcgaatccgtccgatccgaaaactctgcgccccctgttgtatcttgggggaaatgaaaaagagcgaagaggaagggggaagctgaccattttttcttttcatgcgccgaaaaacaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUUGACUGUUUUUAAGUUGAUGAUUCUGUUCAAAGGGUACAUUCAUGAUUGCAUAUUGGCACCAUUCGACAGGUUUUCGUCUCAUAUGGUUAAACAGAAUCGGCCGGAUUUAGUUCCCGAUCGAAUCCGUCCGAUCCGAAAACUCUGCGCCCCCUGUUGUAUCUUGGGGGAAAUGAAAAAGAGCGAAGAGGAAGGGGGAAGCUGACCAUUUUUUCUUUUCAUGCGCCGAAAAACAA .......(((((((..((.(((((((((......))))).)))).))...........(((..((((((.((((((((((.......((......))..(((((.((((((..(((...)))..)))))).))))).))))))).)))))(((((...........))))).)))).........((((((((((((((.......)).))))))))))))....))).))))))). (-63.10) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUGUUUUUCGGCGCAUGAAAAGAAAAAAUGGUCAGCUUCCCCCUUCCUCUUCGCUCUUUUUCAUUUCCCCCAAGAUACAACAGGGGGCGCAGAGUUUUCGGAUCGGACGGAUUCGAUCGGGAACUAAAUCCGGCCGAUUCUGUUUAACCAUAUGAGACGAAAACCUGUCGAAUGGUGCCAAUAUGCAAUCAUGAAUGUACCCUUUGAACAGAAUCAUCAACUUAAAAACAGUCAAUU ((((((((.((.................(((..((.(((((.....((((.((((((((......((......))......)))))))).))))...(((((((.....)))))))..)))))))....)))...((((((((((((........((((......))))....(((((...((((....))))...)))))..)))))))))))).....)).))))))))...... (-59.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 988 140 91 231 182 NC_002950:PG0421|5end_hypothetical_protein_461693..461923_NEGATIVE 412 158 119 131 85 NC_002950:PG0657|5end_Maf-like_protein_707782..708012_NEGATIVE 394 139 95 50 9 NC_002950:PG0736|5end_ribonuclease_HII_785608..785838_POSITIVE 383 165 126 229 184 NC_002950:PG1392|5end_rod_shape-determining_protein_RodA,_putative_1474416..1474646_NEGATIVE 382 149 101 195 149 NC_002950:PG0171|5end_5'-nucleotidase_family_protein_191724..191954_POSITIVE 379 138 99 85 43 NC_002950:PG2209|5end_hypothetical_protein_2320928..2321158_NEGATIVE 370 170 122 50 1 NC_002950:PG2200|5end_TPR_domain_protein_2308807..2309037_NEGATIVE 368 207 163 112 64 NC_002950:PG1871|5end_hypothetical_protein_1966859..1967089_NEGATIVE 365 155 111 230 185 NC_002950:PG0123|5end_hypothetical_protein_144987..145217_POSITIVE 363 210 167 144 110 NC_002950:PG1794|5end_DNA_polymerase_type_I_1885978..1886208_POSITIVE 361 150 102 204 148 NC_002950:PG1719|5end_ABC_transporter,_ATP-binding_protein,_MsbA_family_1806749..1806979_POSITIVE 356 139 96 60 14 NC_002950:PG1753|5end_selenide,_water_dikinase_1838615..1838845_POSITIVE 356 150 102 59 10 NC_002950:PG0054|5end_single-stranded-DNA-specific_exonuclease_RecJ_65065..65295_POSITIVE 355 164 121 165 121 NC_002950:PG0719|5end_sensor_histidine_kinase_772979..773209_NEGATIVE 352 168 121 149 103 NC_002950:PG1944|5end_3-phosphoshikimate_1-carboxyvinyltransferase_2030416..2030646_POSITIVE 351 150 101 114 59 NC_002950:PG1388|5end_hypothetical_protein_1470889..1471119_NEGATIVE 351 140 101 49 3 NC_002950:PG1007|5end_transcriptional_regulator,_GntR_family_1066889..1067119_NEGATIVE 350 226 185 168 126 NC_002950:PG1496|5end_hypothetical_protein_1573342..1573572_POSITIVE 347 135 95 224 176 NC_002950:PG2028|5end_ebsC_protein_2126027..2126257_POSITIVE 347 157 119 181 136 NC_002950:PG1473|5end_conjugative_transposon_protein_TraQ_1550225..1550455_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 523 148 102 52 6 NC_002950:PG0958|3end_ribonuclease_BN,_putative_1018135..1018285_NEGATIVE 441 159 116 119 59 NC_002950:PG0555|3end_DNA-binding_protein,_histone-like_family_611716..611866_NEGATIVE 438 139 93 123 73 NC_002950:PG1961|3end_hypothetical_protein_2048886..2049036_NEGATIVE 415 150 104 130 73 NC_002950:PG0068|3end_hypothetical_protein_82079..82229_POSITIVE 412 158 119 115 69 NC_002950:PG0658|3end_phosphatase,_YrbI_family_707798..707948_NEGATIVE 395 170 121 86 23 NC_002950:PG2044|3end_hypothetical_protein_2144165..2144315_POSITIVE 379 138 99 61 19 NC_002950:PG2210|3end_excinuclease_ABC,_A_subunit_2320952..2321102_NEGATIVE 363 210 167 94 60 NC_002950:PG1793|3end_1,4-alpha-glucan_branching_enzyme_1886008..1886158_POSITIVE 360 141 103 150 117 NC_002950:PG0143|3end_hydrolase,_carbon-nitrogen_family_165747..165897_NEGATIVE 359 160 118 129 79 NC_002950:PG0344|3end_purple_acid_phosphatase_378543..378693_NEGATIVE 358 109 61 151 106 NC_002950:PG1175|3end_ABC_transporter,_ATP-binding_protein,_putative_1254170..1254320_NEGATIVE 358 158 114 69 29 NC_002950:PG0798|3end_ISPg3,_transposase_853827..853977_POSITIVE 357 228 182 108 62 NC_002950:PG1690|3end_Sua5/YciO/YrdC/YwlC_family_protein_1775171..1775321_NEGATIVE 357 227 184 114 64 NC_002950:PG0678|3end_pyrazinamidase/nicotinamidase,_putative_729471..729621_POSITIVE 356 173 132 139 98 NC_002950:PG2040|3end_DNA-binding_protein,_histone-like_family_2138398..2138548_NEGATIVE 356 139 96 63 17 NC_002950:PG1752|3end_hypothetical_protein_1838698..1838848_POSITIVE 351 150 101 133 78 NC_002950:PG1389|3end_DNA-binding_protein,_histone-like_family_1470870..1471020_NEGATIVE 351 140 101 52 6 NC_002950:PG1008|3end_hypothetical_protein_1066886..1067036_NEGATIVE 348 139 100 39 3 NC_002950:PG0735|3end_aminotransferase,_class_V_785677..785827_POSITIVE 346 149 101 53 4 NC_002950:PG0144|3end_hypothetical_protein_166643..166793_NEGATIVE