Origin IGS: cggtttctaaaaactcttttttatatgtaatgctgcaaagttacgattatccacaaagggatcagccgaaactgtacaggttttcatatctctgcacagtttcggctgctatatcttttcattaggggatactccgaaatgctattccttattgcttgtgcaaaaaaggaaacagctgcta .........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 tagcagctgtttccttttttgcacaagcaataaggaatagcatttcggagtatcccctaatgaaaagatatagcagccgaaactgtgcagagatatgaaaacctgtacagtttcggctgatccctttgtggataatcgtaactttgcagcattacatataaaaaagagtttttagaaaccg Mask Tandem Repeat Region ================================================ cggtttctaaaaactcttttttatatgtaatgctgcaaagttacgattatccacaaagggatcagccgaaactgtacaggttttcatatctctgcacagtttcggctgctatatcttttcattaggggatactccgaaatgctattccttattgcttgtgcaaaaaaggaaacagctgcta Find is-nt database================================================ Query_seq: PG0160:PG0161|PG0160:PG0161:hypothetical protein:hypothetical protein:<-<-:184176..184356 181 cggtttctaaaaactcttttttatatgtaatgctgcaaagttacgattatccacaaagggatcagccgaaactgtacaggttttcatatctctgcacagtttcggctgctatatcttttcattaggggatactccgaaatgctattccttattgcttgtgcaaaaaaggaaacagctgcta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG0160:PG0161|PG0160:PG0161:hypothetical protein:hypothetical protein:<-<-:184176..184356 181 cggtttctaaaaactcttttttatatgtaatgctgcaaagttacgattatccacaaagggatcagccgaaactgtacaggttttcatatctctgcacagtttcggctgctatatcttttcattaggggatactccgaaatgctattccttattgcttgtgcaaaaaaggaaacagctgcta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG0160:PG0161|PG0160:PG0161:hypothetical protein:hypothetical protein:<-<-:184176..184356 181 cggtttctaaaaactcttttttatatgtaatgctgcaaagttacgattatccacaaagggatcagccgaaactgtacaggttttcatatctctgcacagtttcggctgctatatcttttcattaggggatactccgaaatgctattccttattgcttgtgcaaaaaaggaaacagctgcta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 cggtttctaaaaactcttttttatatgtaatgctgcaaagttacgattatccacaaagggatcagccgaaactgtacaggttttcatatctctgcacagtttcggctgctatatcttttcattaggggatactccgaaatgctattccttattgcttgtgcaaaaaaggaaacagctgcta Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: + Start: 30 End: 122 ............................. M L Q S Y D Y P Q R D Q P K L Y R F S Y L C T V S A A I S F H ........................................................... Protein_Len: 45 Strand: + Start: 46 End: 180 ............................................. M I H K G I S R N C T G F H I S A Q F R L L Y L F I R G Y S E M L F L I A C A K K E T A A . Protein_Len: 53 Strand: + Start: 23 End: 181 ...................... M C N A A K L R L S T K G S A E T V Q V F I S L H S F G C Y I F S L G D T P K C Y S L L L V Q K R K Q L L Protein_Len: 30 Strand: - Start: 10 End: 99 ......... F S K K I H L A A F N R N D V F P D A S V T C T K M D R C M .................................................................................. cggtttctaaaaactcttttttatatgtaatgctgcaaagttacgattatccacaaagggatcagccgaaactgtacaggttttcatatctctgcacagtttcggctgctatatcttttcattaggggatactccgaaatgctattccttattgcttgtgcaaaaaaggaaacagctgcta 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================================================ cggtttctaaaaactcttttttatatgtaatgctgcaaagttacgattatccacaaagggatcagccgaaactgtacaggttttcatatctctgcacagtttcggctgctatatcttttcattaggggatactccgaaatgctattccttattgcttgtgcaaaaaaggaaacagctgcta Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 53 HP_score: -3.3 Tail_Score: -3.8125 Start: 58 End: 113 Full_Region: ACGATTATCCACAAA GGGATCAGCCGAAACTGTACAGGTT TTCAT ATCTCTGCACAGTTTCGGCTGCTATA TCTTTTCATTAGGGG .........................................................GGGATCAGCCGAAACTGTACAGGTTTTCATATCTCTGCACAGTTTCGGCTGCTATA.................................................................... TransTerm Strand: - Conf: 55 HP_score: -3.3 Tail_Score: -3.93963 Start: 58 End: 113 Full_Region: cccctaatgaaaaga tatagcagccgaaactgtgcagagat atgaa aacctgtacagtttcggctgatccc tttgtggataatcgt .........................................................tatagcagccgaaactgtgcagagatatgaaaacctgtacagtttcggctgatccc.................................................................... TransTerm Strand: + Conf: 71 HP_score: -8.1 Tail_Score: -3.48718 Start: 60 End: 111 Full_Region: GATTATCCACAAAGG GATCAGCCGAAACTGTACAGGTT TTCAT ATCTCTGCACAGTTTCGGCTGCTA TATCTTTTCATTAGG ...........................................................GATCAGCCGAAACTGTACAGGTTTTCATATCTCTGCACAGTTTCGGCTGCTA...................................................................... TransTerm Strand: + Conf: 79 HP_score: -10.7 Tail_Score: -3.30572 Start: 62 End: 109 Full_Region: TTATCCACAAAGGGA TCAGCCGAAACTGTACAGGTT TTCAT ATCTCTGCACAGTTTCGGCTGC TATATCTTTTCATTA .............................................................TCAGCCGAAACTGTACAGGTTTTCATATCTCTGCACAGTTTCGGCTGC........................................................................ TransTerm Strand: - Conf: 89 HP_score: -12.9 Tail_Score: -2.71325 Start: 62 End: 109 Full_Region: taatgaaaagatata gcagccgaaactgtgcagagat atgaa aacctgtacagtttcggctga tccctttgtggataa .............................................................gcagccgaaactgtgcagagatatgaaaacctgtacagtttcggctga........................................................................ TransTerm Strand: + Conf: 95 HP_score: -14.2 Tail_Score: -2.57259 Start: 63 End: 108 Full_Region: TATCCACAAAGGGAT CAGCCGAAACTGTACAGGTT TTCAT ATCTCTGCACAGTTTCGGCTG CTATATCTTTTCATT ..............................................................CAGCCGAAACTGTACAGGTTTTCATATCTCTGCACAGTTTCGGCTG......................................................................... TransTerm Strand: + Conf: 78 HP_score: -11.0 Tail_Score: -2.80859 Start: 65 End: 106 Full_Region: TCCACAAAGGGATCA GCCGAAACTGTACAGGTT TTCAT ATCTCTGCACAGTTTCGGC TGCTATATCTTTTCA ................................................................GCCGAAACTGTACAGGTTTTCATATCTCTGCACAGTTTCGGC........................................................................... Find igs database================================================ Query_seq: PG0160:PG0161|PG0160:PG0161:hypothetical protein:hypothetical protein:<-<-:184176..184356 181 cggtttctaaaaactcttttttatatgtaatgctgcaaagttacgattatccacaaagggatcagccgaaactgtacaggttttcatatctctgcacagtttcggctgctatatcttttcattaggggatactccgaaatgctattccttattgcttgtgcaaaaaaggaaacagctgcta Intra-Species Hit: Count: 1 Min: 1 Max: 181 Len: 181 Subject: NC_002950_PG0160_PG0161|hypothetical protein:hypothetical protein|NEGATIVE:NEGATIVE|[184176,184356]|181 HSP 1 e-value: 2.0E-98 bit: 359.0 Len: 181 Query Start:1 Query End:181 Subject Strand: POSITIVE Subject Start: 1 Subject End: 181 cggtttctaaaaactcttttttatatgtaatgctgcaaagttacgattatccacaaagggatcagccgaaactgtacaggttttcatatctctgcacagtttcggctgctatatcttttcattaggggatactccgaaatgctattccttattgcttgtgcaaaaaaggaaacagctgcta cggtttctaaaaactcttttttatatgtaatgctgcaaagttacgattatccacaaagggatcagccgaaactgtacaggttttcatatctctgcacagtttcggctgctatatcttttcattaggggatactccgaaatgctattccttattgcttgtgcaaaaaaggaaacagctgcta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CGGUUUCUAAAAACUCUUUUUUAUAUGUAAUGCUGCAAAGUUACGAUUAUCCACAAAGGGAUCAGCCGAAACUGUACAGGUUUUCAUAUCUCUGCACAGUUUCGGCUGCUAUAUCUUUUCAUUAGGGGAUACUCCGAAAUGCUAUUCCUUAUUGCUUGUGCAAAAAAGGAAACAGCUGCUA (((......................((((((........))))))..(((((...((((((((((((((((((((.((((..........)))).)))))))))))))....))))))).......)))))..)))....(((.((((((.((((....))))..))))))..)))..... (-49.60) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAGCAGCUGUUUCCUUUUUUGCACAAGCAAUAAGGAAUAGCAUUUCGGAGUAUCCCCUAAUGAAAAGAUAUAGCAGCCGAAACUGUGCAGAGAUAUGAAAACCUGUACAGUUUCGGCUGAUCCCUUUGUGGAUAAUCGUAACUUUGCAGCAUUACAUAUAAAAAAGAGUUUUUAGAAACCG .....((((((.((((..((((....)))).))))))))))....(((.........(((((.((((.(((..(((((((((((((((((............)))))))))))))))))((((......))))....))).))))....)))))....((((((....))))))....))) (-54.50) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 955 110 61 201 152 NC_002950:PG0160|5end_hypothetical_protein_184085..184315_NEGATIVE 357 109 61 84 29 NC_002950:PG0246|5end_hypothetical_protein_281241..281471_NEGATIVE 356 179 131 62 14 NC_002950:PG1959|5end_ribosomal_protein_L33_2048405..2048635_NEGATIVE 325 110 61 182 137 NC_002950:PG1116|5end_methylenetetrahydrofolate_dehydrogenase/methenyltetrahydrofolate_cyclohydrolase_1188931..1189161_POSITIVE 318 110 65 50 6 NC_002950:PG1346|5end_glycosyl_transferase,_group_1_family_protein_1426708..1426938_POSITIVE 317 137 93 61 15 NC_002950:PG1596|5end_isoleucyl-tRNA_synthetase,_putative_1674543..1674773_POSITIVE 317 110 67 169 118 NC_002950:PG0986|5end_hypothetical_protein_1047426..1047656_POSITIVE 307 137 97 215 172 NC_002950:PG0165|5end_heat_shock_protein_15_187807..188037_NEGATIVE 303 78 31 87 38 NC_002950:PG1898|5end_transporter,_putative_1997335..1997565_NEGATIVE 302 99 59 217 179 NC_002950:PG2101|5end_hypothetical_protein_2211273..2211503_NEGATIVE 302 138 92 120 72 NC_002950:PG1752|5end_hypothetical_protein_1838394..1838624_POSITIVE 301 110 64 86 26 NC_002950:PG1619|5end_biotin_synthesis_protein_BioC,_putative_1698568..1698798_POSITIVE 299 149 102 186 127 NC_002950:PG0562|5end_potassium_uptake_protein_TrkA,_putative_619222..619452_POSITIVE 295 105 61 173 121 NC_002950:PG1072|5end_MutS_family_protein_1138976..1139206_POSITIVE 293 120 72 230 174 NC_002950:PG1269|5end_delta-1-pyrroline-5-carboxylate_dehydrogenase_1349201..1349431_NEGATIVE 291 109 64 105 61 NC_002950:PG0017|5end_sensor_histidine_kinase_18307..18537_POSITIVE 288 125 81 94 46 NC_002950:PG1240|5end_transcriptional_regulator,_tetR_family_1315061..1315291_NEGATIVE 287 169 125 220 174 NC_002950:PG1185|5end_hypothetical_protein_1267752..1267982_NEGATIVE 287 109 62 156 88 NC_002950:PG0171|5end_5'-nucleotidase_family_protein_191724..191954_POSITIVE 284 137 99 208 163 NC_002950:PG0447|5end_hypothetical_protein_487278..487508_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 325 110 61 58 13 NC_002950:PG1115|3end_signal_recognition_particle_protein_1188887..1189037_POSITIVE 318 110 65 53 9 NC_002950:PG1345|3end_glycosyl_transferase,_group_1_family_protein_1426791..1426941_POSITIVE 307 179 139 43 2 NC_002950:PG1960|3end_ribosomal_protein_L28_2048424..2048574_NEGATIVE 306 136 103 36 2 NC_002950:PG0076|3end_N-acetylmuramoyl-L-alanine_amidase,_family_4_90392..90542_NEGATIVE 303 78 31 82 33 NC_002950:PG1899|3end_TonB-dependent_receptor,_putative_1997340..1997490_NEGATIVE 303 109 61 117 64 NC_002950:PG0711|3end_hypothetical_protein_766281..766431_POSITIVE 302 99 59 66 28 NC_002950:PG2102|3end_immunoreactive_61_kDa_antigen_PG91_2211424..2211574_NEGATIVE 302 138 92 136 88 NC_002950:PG1751|3end_aminotransferase,_class_V_1838490..1838640_POSITIVE 301 110 64 107 47 NC_002950:PG1618|3end_hypothetical_protein_1698669..1698819_POSITIVE 299 107 62 146 102 NC_002950:PG2105|3end_lipoprotein,_putative_2214579..2214729_POSITIVE 297 135 93 65 20 NC_002950:PG0721|3end_NLP/P60_family_protein_774535..774685_POSITIVE 294 110 61 66 15 NC_002950:PG1967|3end_TPR_domain_protein_2058135..2058285_POSITIVE 291 109 64 94 50 NC_002950:PG0016|3end_sigma-54_dependent_DNA-binding_response_regulator_18376..18526_POSITIVE 288 130 82 138 89 NC_002950:PG0297|3end_hypothetical_protein_335297..335447_NEGATIVE 287 106 66 114 76 NC_002950:PG1416|3end_enoyl-(acyl-carrier-protein)_reductase_II_1501078..1501228_POSITIVE 287 109 62 126 58 NC_002950:PG0170|3end_methionyl-tRNA_synthetase_191774..191924_POSITIVE 285 77 38 139 95 NC_002950:PG1414|3end_hypothetical_protein_1499704..1499854_POSITIVE 284 130 94 72 38 NC_002950:PG1897|3end_thiamin_pyrophosphokinase_catalytic_domain_protein_1996053..1996203_NEGATIVE 282 130 86 56 1 NC_002950:PG1079|3end_enoyl-CoA_hydratase/isomerase_family_protein_1147399..1147549_POSITIVE 279 99 51 133 78 NC_002950:PG1229|3end_hypothetical_protein_1305559..1305709_NEGATIVE