Origin IGS: taaatcagcacagatttgtttggaaggtgaagtagtccgacctcacacatcataaaaagaaggtgtactatacaaagctataaacgtataagttacgaagagaagagggtatatcacaaagtgatttcaccctctttttttgtatcatcagggaaagagaaataaatcctttccctttttct .........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 agaaaaagggaaaggatttatttctctttccctgatgatacaaaaaaagagggtgaaatcactttgtgatataccctcttctcttcgtaacttatacgtttatagctttgtatagtacaccttctttttatgatgtgtgaggtcggactacttcaccttccaaacaaatctgtgctgattta Mask Tandem Repeat Region ================================================ taaatcagcacagatttgtttggaaggtgaagtagtccgacctcacacatcataaaaagaaggtgtactatacaaagctataaacgtataagttacgaagagaagagggtatatcacaaagtgatttcaccctctttttttgtatcatcagggaaagagaaataaatcctttccctttttct Find is-nt database================================================ Query_seq: TF1707:TF1708|TF1707:TF1708:conserved hypothetical protein:transcriptional regulator:->->:1829143..1829324 182 taaatcagcacagatttgtttggaaggtgaagtagtccgacctcacacatcataaaaagaaggtgtactatacaaagctataaacgtataagttacgaagagaagagggtatatcacaaagtgatttcaccctctttttttgtatcatcagggaaagagaaataaatcctttccctttttct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF1707:TF1708|TF1707:TF1708:conserved hypothetical protein:transcriptional regulator:->->:1829143..1829324 182 taaatcagcacagatttgtttggaaggtgaagtagtccgacctcacacatcataaaaagaaggtgtactatacaaagctataaacgtataagttacgaagagaagagggtatatcacaaagtgatttcaccctctttttttgtatcatcagggaaagagaaataaatcctttccctttttct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF1707:TF1708|TF1707:TF1708:conserved hypothetical protein:transcriptional regulator:->->:1829143..1829324 182 taaatcagcacagatttgtttggaaggtgaagtagtccgacctcacacatcataaaaagaaggtgtactatacaaagctataaacgtataagttacgaagagaagagggtatatcacaaagtgatttcaccctctttttttgtatcatcagggaaagagaaataaatcctttccctttttct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taaatcagcacagatttgtttggaaggtgaagtagtccgacctcacacatcataaaaagaaggtgtactatacaaagctataaacgtataagttacgaagagaagagggtatatcacaaagtgatttcaccctctttttttgtatcatcagggaaagagaaataaatcctttccctttttct Predict ORF larger than 30AA ================================================ Protein_Len: 38 Strand: + Start: 49 End: 162 ................................................ M I K R R C T I Q S Y K R I S Y E E K R V Y H K V I S P S F F V S S G K E K .................... Protein_Len: 31 Strand: - Start: 71 End: 163 ...................................................................... V F S Y V Y L N R L S S P I D C L S K V R K K Q I M L S L S M ................... taaatcagcacagatttgtttggaaggtgaagtagtccgacctcacacatcataaaaagaaggtgtactatacaaagctataaacgtataagttacgaagagaagagggtatatcacaaagtgatttcaccctctttttttgtatcatcagggaaagagaaataaatcctttccctttttct 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================================================ taaatcagcacagatttgtttggaaggtgaagtagtccgacctcacacatcataaaaagaaggtgtactatacaaagctataaacgtataagttacgaagagaagagggtatatcacaaagtgatttcaccctctttttttgtatcatcagggaaagagaaataaatcctttccctttttct Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 100 HP_score: -8.7 Tail_Score: -5.74122 Start: 105 End: 134 Full_Region: AAGTTACGAAGAGAA GAGGGTATATCAC AAA GTGATTTCACCCTC TTTTTTTGTATCATC ........................................................................................................GAGGGTATATCACAAAGTGATTTCACCCTC................................................ TransTerm Strand: - Conf: 78 HP_score: -8.7 Tail_Score: -3.724 Start: 105 End: 134 Full_Region: gatgatacaaaaaaa gagggtgaaatcac ttt gtgatataccctc ttctcttcgtaactt ........................................................................................................gagggtgaaatcactttgtgatataccctc................................................ Find igs database================================================ Query_seq: TF1707:TF1708|TF1707:TF1708:conserved hypothetical protein:transcriptional regulator:->->:1829143..1829324 182 taaatcagcacagatttgtttggaaggtgaagtagtccgacctcacacatcataaaaagaaggtgtactatacaaagctataaacgtataagttacgaagagaagagggtatatcacaaagtgatttcaccctctttttttgtatcatcagggaaagagaaataaatcctttccctttttct Intra-Species Hit: Count: 1 Min: 1 Max: 182 Len: 182 Subject: tfor_TF1707_TF1708|conserved hypothetical protein:transcriptional regulator|POSITIVE:POSITIVE|[1829143,1829324]|182 HSP 1 e-value: 2.0E-86 bit: 319.0 Len: 182 Query Start:1 Query End:182 Subject Strand: POSITIVE Subject Start: 1 Subject End: 182 taaatcagcacagatttgtttggaaggtgaagtagtccgacctcacacatcataaaaagaaggtgtactatacaaagctataaacgtataagttacgaagagaagagggtatatcacaaagtgatttcaccctcnnnnnnngtatcatcagggaaagagaaataaatcctttccctttttct taaatcagcacagatttgtttggaaggtgaagtagtccgacctcacacatcataaaaagaaggtgtactatacaaagctataaacgtataagttacgaagagaagagggtatatcacaaagtgatttcaccctctttttttgtatcatcagggaaagagaaataaatcctttccctttttct Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAAUCAGCACAGAUUUGUUUGGAAGGUGAAGUAGUCCGACCUCACACAUCAUAAAAAGAAGGUGUACUAUACAAAGCUAUAAACGUAUAAGUUACGAAGAGAAGAGGGUAUAUCACAAAGUGAUUUCACCCUCUUUUUUUGUAUCAUCAGGGAAAGAGAAAUAAAUCCUUUCCCUUUUUCU .......((((...(((...(((...((((.((......)).))))...)))...)))....))))...((((((.........((((.....))))..(((((((((((..(((((...)))))...)))))))))))))))))....((((((((.((......))))))))))...... (-47.50) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGAAAAAGGGAAAGGAUUUAUUUCUCUUUCCCUGAUGAUACAAAAAAAGAGGGUGAAAUCACUUUGUGAUAUACCCUCUUCUCUUCGUAACUUAUACGUUUAUAGCUUUGUAUAGUACACCUUCUUUUUAUGAUGUGUGAGGUCGGACUACUUCACCUUCCAAACAAAUCUGUGCUGAUUUA ......((((((((((......)).))))))))....(((((((..(((((((((..(((((...))))).))))))))).....((((.....))))........)))))))((((((..((..(((...((.(.(((((((......)))))))).)).)))..))..))))))...... (-46.20) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 332 138 92 52 5 tfor:TF2577|5end_30S_ribosomal_protein_S13_2746308..2746538_POSITIVE 323 140 96 218 173 tfor:TF1534|5end_conserved_hypothetical_protein_1639485..1639715_POSITIVE 315 139 92 229 175 tfor:TF1999|5end_ArgK_protein_with_ATPase_and_kinase_domains_2152769..2152999_POSITIVE 312 144 102 221 172 tfor:TF1505|5end_conserved_hypothetical_protein_1610773..1611003_POSITIVE 309 140 97 132 95 tfor:TF1251|5end_riboflavin_synthase,_alpha_subunit_1333744..1333974_POSITIVE 307 137 93 228 178 tfor:TF0184|5end_dihydroneopterin_aldolase_195629..195859_POSITIVE 292 138 96 78 30 tfor:TF1046|5end_hypothetical_protein_1108178..1108408_POSITIVE 286 48 3 217 179 tfor:TF2615|5end_conserved_hypothetical_protein_2790569..2790799_POSITIVE 270 134 94 88 30 tfor:TF2503|5end_conserved_hypothetical_protein_2678430..2678660_POSITIVE 269 49 3 162 125 tfor:TF2778|5end_outer_membrane_protein,__TonB_dependent_receptor_2961823..2962053_POSITIVE 267 42 10 47 4 tfor:TF0095|5end_methyltransferase_105893..106123_POSITIVE 266 179 142 165 126 tfor:TF3078|5end_ribonucleoside_diphosphate_reductase,_alpha_subunit_3306609..3306839_POSITIVE 266 146 102 209 160 tfor:TF2593|5end_amino_acid_transport_protein_2762882..2763112_POSITIVE 265 145 101 200 158 tfor:TF1594|5end_hypothetical_protein_1709903..1710133_POSITIVE 261 44 11 194 166 tfor:TF2900|5end_conserved_hypothetical_protein_3088252..3088482_POSITIVE 261 49 2 100 34 tfor:TF1941|5end_3-phosphoshikimate-1-carboxyvinyltransferase_2088862..2089092_POSITIVE 258 102 78 146 119 tfor:TF1359|5end_hypothetical_protein_1438977..1439207_POSITIVE 255 142 101 172 128 tfor:TF0216|5end_50S_ribosomal_protein_L20_242476..242706_POSITIVE 255 48 11 182 135 tfor:TF0100|5end_conserved_hypothetical_protein_111135..111365_POSITIVE 254 133 96 51 6 tfor:TF3024|5end_periplasmic_protease_3247204..3247434_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 323 140 96 68 23 tfor:TF1532|3end_potassium_uptake_system_protein_1639415..1639565_POSITIVE 315 139 92 66 12 tfor:TF1997|3end_ROK_family_transcriptional_regulator_2152686..2152836_POSITIVE 309 140 97 109 72 tfor:TF1250|3end_possible_cation_efflux_pump_1333801..1333951_POSITIVE 297 137 99 47 2 tfor:TF0182|3end_DNA-binding_protein,_HU-related_195528..195678_POSITIVE 292 138 96 65 17 tfor:TF1045|3end_conserved_hypothetical_protein_1108245..1108395_POSITIVE 284 160 118 109 67 tfor:TF0066|3end_conserved_hypothetical_protein_73121..73271_POSITIVE 273 120 72 101 55 tfor:TF0358|3end_hypothetical_protein_376304..376454_POSITIVE 270 134 94 69 11 tfor:TF2502|3end_conserved_hypothetical_protein_2678491..2678641_POSITIVE 269 49 3 72 35 tfor:TF2776|3end_hypothetical_protein_2961813..2961963_POSITIVE 266 146 102 54 5 tfor:TF2592|3end_conserved_hypothetical_protein_2762807..2762957_POSITIVE 261 132 95 128 88 tfor:TF1633|3end_mobilizable_transposon,_excision_protein_1745348..1745498_POSITIVE 255 48 11 91 44 tfor:TF0099|3end_glycosyltransferase_of_PMT_family_111124..111274_POSITIVE 254 133 96 68 23 tfor:TF3022|3end_chorismate_synthase_3247301..3247451_POSITIVE 254 110 62 44 3 tfor:TF1331|3end_outer_membrane_protein_1410934..1411084_POSITIVE 249 170 122 48 8 tfor:TF0178|3end_ferritin_188223..188373_POSITIVE 246 41 6 76 45 tfor:TF2087|3end_conserved_hypothetical_protein_2257694..2257844_POSITIVE 242 155 119 125 82 tfor:TF1682|3end_hydrolase_1797343..1797493_POSITIVE 241 144 101 62 22 tfor:TF2804|3end_conserved_hypothetical_protein_2994449..2994599_POSITIVE 240 42 5 117 88 tfor:TF0279|3end_conserved_hypothetical_protein_308679..308829_POSITIVE 239 43 7 59 18 tfor:TF2154|3end_conserved_hypothetical_protein_2329529..2329679_POSITIVE