Origin IGS: taagcccgacggcggtgtgtcataacgggcgaactgcttcgttgcttgcggaatgcaagctcggtcacatacgttagtatgctccctcgttcgcatccttagcgccttgcatttcacctattctgacacacctaaaaagggtggtctcaaacattgtgttttatataccctcaaagtgttcggaattttgctaattttgccaaaaaaaacgatacg .........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 cgtatcgttttttttggcaaaattagcaaaattccgaacactttgagggtatataaaacacaatgtttgagaccaccctttttaggtgtgtcagaataggtgaaatgcaaggcgctaaggatgcgaacgagggagcatactaacgtatgtgaccgagcttgcattccgcaagcaacgaagcagttcgcccgttatgacacaccgccgtcgggctta Mask Tandem Repeat Region ================================================ taagcccgacggcggtgtgtcataacgggcgaactgcttcgttgcttgcggaatgcaagctcggtcacatacgttagtatgctccctcgttcgcatccttagcgccttgcatttcacctattctgacacacctaaaaagggtggtctcaaacattgtgttttatataccctcaaagtgttcggaattttgctaattttgccaaaaaaaacgatacg Find is-nt database================================================ Query_seq: TF0145:TF0146|TF0145:TF0146:glutamine synthetase:glutamine-dependent NAD(+) synthetase:->->:154779..154994 216 taagcccgacggcggtgtgtcataacgggcgaactgcttcgttgcttgcggaatgcaagctcggtcacatacgttagtatgctccctcgttcgcatccttagcgccttgcatttcacctattctgacacacctaaaaagggtggtctcaaacattgtgttttatataccctcaaagtgttcggaattttgctaattttgccaaaaaaaacgatacg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF0145:TF0146|TF0145:TF0146:glutamine synthetase:glutamine-dependent NAD(+) synthetase:->->:154779..154994 216 taagcccgacggcggtgtgtcataacgggcgaactgcttcgttgcttgcggaatgcaagctcggtcacatacgttagtatgctccctcgttcgcatccttagcgccttgcatttcacctattctgacacacctaaaaagggtggtctcaaacattgtgttttatataccctcaaagtgttcggaattttgctaattttgccaaaaaaaacgatacg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF0145:TF0146|TF0145:TF0146:glutamine synthetase:glutamine-dependent NAD(+) synthetase:->->:154779..154994 216 taagcccgacggcggtgtgtcataacgggcgaactgcttcgttgcttgcggaatgcaagctcggtcacatacgttagtatgctccctcgttcgcatccttagcgccttgcatttcacctattctgacacacctaaaaagggtggtctcaaacattgtgttttatataccctcaaagtgttcggaattttgctaattttgccaaaaaaaacgatacg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taagcccgacggcggtgtgtcataacgggcgaactgcttcgttgcttgcggaatgcaagctcggtcacatacgttagtatgctccctcgttcgcatccttagcgccttgcatttcacctattctgacacacctaaaaagggtggtctcaaacattgtgttttatataccctcaaagtgttcggaattttgctaattttgccaaaaaaaacgatacg Predict ORF larger than 30AA ================================================ Protein_Len: 54 Strand: + Start: 53 End: 214 .................................................... M Q A R S H T L V C S L V R I L S A L H F T Y S D T P K K G G L K H C V L Y T L K V F G I L L I L P K K T I .. Protein_Len: 31 Strand: - Start: 121 End: 213 ........................................................................................................................ E S V G L F P P R L C Q T K Y V R L T N P I K S I K G F F V M ... Protein_Len: 39 Strand: - Start: 1 End: 117 L G S P P T D Y R A F Q K T A Q P I C A R D C V N T H E R T R M R L A K C K M ................................................................................................... taagcccgacggcggtgtgtcataacgggcgaactgcttcgttgcttgcggaatgcaagctcggtcacatacgttagtatgctccctcgttcgcatccttagcgccttgcatttcacctattctgacacacctaaaaagggtggtctcaaacattgtgttttatataccctcaaagtgttcggaattttgctaattttgccaaaaaaaacgatacg 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================================================ taagcccgacggcggtgtgtcataacgggcgaactgcttcgttgcttgcggaatgcaagctcggtcacatacgttagtatgctccctcgttcgcatccttagcgccttgcatttcacctattctgacacacctaaaaagggtggtctcaaacattgtgttttatataccctcaaagtgttcggaattttgctaattttgccaaaaaaaacgatacg Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TF0145:TF0146|TF0145:TF0146:glutamine synthetase:glutamine-dependent NAD(+) synthetase:->->:154779..154994 216 taagcccgacggcggtgtgtcataacgggcgaactgcttcgttgcttgcggaatgcaagctcggtcacatacgttagtatgctccctcgttcgcatccttagcgccttgcatttcacctattctgacacacctaaaaagggtggtctcaaacattgtgttttatataccctcaaagtgttcggaattttgctaattttgccaaaaaaaacgatacg Intra-Species Hit: Count: 4 Min: 1 Max: 201 Len: 201 Subject: tfor_TF0145_TF0146|glutamine synthetase:glutamine-dependent NAD(+) synthetase|POSITIVE:POSITIVE|[154779,154994]|216 HSP 1 e-value: 1.0E-110 bit: 398.0 Len: 201 Query Start:1 Query End:201 Subject Strand: POSITIVE Subject Start: 1 Subject End: 201 taagcccgacggcggtgtgtcataacgggcgaactgcttcgttgcttgcggaatgcaagctcggtcacatacgttagtatgctccctcgttcgcatccttagcgccttgcatttcacctattctgacacacctaaaaagggtggtctcaaacattgtgttttatataccctcaaagtgttcggaattttgctaattttgcc............... taagcccgacggcggtgtgtcataacgggcgaactgcttcgttgcttgcggaatgcaagctcggtcacatacgttagtatgctccctcgttcgcatccttagcgccttgcatttcacctattctgacacacctaaaaagggtggtctcaaacattgtgttttatataccctcaaagtgttcggaattttgctaattttgcc............... Subject: tfor_TF0983_TF0984|nitroreductase family protein, possible NADH dehydrogenase/NAD(P)H nitroreductase:possible mucin-desulfating sulfatase (MdsC protein)|POSITIVE:POSITIVE|[1040095,1040398]|304 HSP 1 e-value: 1.0E-32 bit: 141.0 Len: 126 Query Start:18 Query End:143 Subject Strand: NEGATIVE Subject Start: 142 Subject End: 268 .................tgtcataacgggcgaactgcttcgttgcttgcggaatgcaagctcggtcacatacgttagtatgctccctcgttcgcatccttagcgccttgc-atttcacctattctgacacacctaaaaagggtg......................................................................... .................tgtcataacgagcgaactgcttcgttgtttgcggaatgcgagctcggccacatacgttagtatgctccctcgctctcatccttagcgcctcccaatttcacccattcttacatacctaaagagggtg......................................................................... Subject: tfor_TF0795_TF0797|hypothetical protein:conserved hypothetical protein|POSITIVE:POSITIVE|[853260,853435]|176 HSP 1 e-value: 2.0E-28 bit: 127.0 Len: 108 Query Start:11 Query End:118 Subject Strand: POSITIVE Subject Start: 15 Subject End: 122 ..........ggcggtgtgtcataacgggcgaactgcttcgttgcttgcggaatgcaagctcggtcacatacgttagtatgctccctcgttcgcatccttagcgccttgcatttcacc.................................................................................................. ..........ggcggtgtgtcataacgggcgaactgcttcgttgcttacggaatgcgtgctcggttacataccttagtatactccctcgctctcatccttaattccttgcatttcacc.................................................................................................. Subject: tfor_TF0475_TF0476|possible transcriptional regulator, AraC family:conserved hypothetical protein|POSITIVE:POSITIVE|[494886,495083]|198 HSP 1 e-value: 3.0E-27 bit: 123.0 Len: 142 Query Start:21 Query End:162 Subject Strand: POSITIVE Subject Start: 14 Subject End: 155 ....................cataacgggcgaactgcttcgttgcttgcggaatgcaagctcggtcacatacgttagtatgctccctcgttcgcatccttagcgccttgcatttcacctattctgacacacctaaaaagggtggtctcaaacattgtgtttt...................................................... ....................cataacgggagaactgcttcgtttcctgctgaatgtaaactcggtcatatacgtttgtatactccctcgctctcatccttagcgtcttgcatttcacccatgcttacacacctaaagagggtgtgcccaaacattgcgtttt...................................................... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAGCCCGACGGCGGUGUGUCAUAACGGGCGAACUGCUUCGUUGCUUGCGGAAUGCAAGCUCGGUCACAUACGUUAGUAUGCUCCCUCGUUCGCAUCCUUAGCGCCUUGCAUUUCACCUAUUCUGACACACCUAAAAAGGGUGGUCUCAAACAUUGUGUUUUAUAUACCCUCAAAGUGUUCGGAAUUUUGCUAAUUUUGCC .....((((((..(((((((((.((..((.(((.(((...((.(((...(((.(((.(((..((...(((((....)))))...))..))).))))))..)))))...))).))).))..)).))))))))).....((((((.....((((.....))))....)))))).....)).))))......((.......)). (-61.00) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GGCAAAAUUAGCAAAAUUCCGAACACUUUGAGGGUAUAUAAAACACAAUGUUUGAGACCACCCUUUUUAGGUGUGUCAGAAUAGGUGAAAUGCAAGGCGCUAAGGAUGCGAACGAGGGAGCAUACUAACGUAUGUGACCGAGCUUGCAUUCCGCAAGCAACGAAGCAGUUCGCCCGUUAUGACACACCGCCGUCGGGCUUA .((.......)).....(((((.......((((((.....((((.....))))......))))))....(((((((((.((..((((((.(((..(..(((..((((((((.(..((..((((((....))))))..))..).))))).)))...)))..)...))).))))))..)).)))))))))....))))).... (-74.00) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 917 68 21 225 178 tfor:TF0663|5end_conserved_hypothetical_protein_708450..708680_POSITIVE 917 68 21 91 44 tfor:TF0662|5end_hypothetical_protein_708316..708546_POSITIVE 882 107 61 217 171 tfor:TF0984|5end_possible_mucin-desulfating_sulfatase_(MdsC_protein)_1040259..1040489_POSITIVE 493 38 5 229 196 tfor:TF1586|5end_hypothetical_protein_1690971..1691201_POSITIVE 485 49 1 57 10 tfor:TF2633|5end_ABC_transporter,_ATP-binding_protein/permease_component_2802013..2802243_POSITIVE 466 50 5 47 7 tfor:TF0351|5end_hypothetical_protein_370922..371152_POSITIVE 452 60 11 204 149 tfor:TF3019|5end_tRNA_and_rRNA_cytosine-C5-methylase_3242164..3242394_POSITIVE 444 160 116 198 154 tfor:TF1505|5end_conserved_hypothetical_protein_1610773..1611003_POSITIVE 444 172 131 74 28 tfor:TF1046|5end_hypothetical_protein_1108178..1108408_POSITIVE 440 60 12 58 6 tfor:TF2020|5end_muconate_cycloisomerase_2176321..2176551_POSITIVE 439 50 4 136 94 tfor:TF0215|5end_tRNA/rRNA_methyltransferase,_TrmH_family_241463..241693_POSITIVE 410 48 4 212 169 tfor:TF0810|5end_possible_outer_membrane_efflux_protein_868438..868668_POSITIVE 408 50 4 193 152 tfor:TF2775|5end_conserved_hypothetical_protein;_possible_mucoidy_inhibitor-related_protein_2959668..2959898_POSITIVE 407 50 10 31 1 tfor:TF1909|5end_cobalamin_(5`-phosphate)_synthase_2063207..2063437_POSITIVE 405 170 121 157 104 tfor:TF0187|5end_ferredoxin_202151..202381_POSITIVE 403 50 7 43 5 tfor:TF1688|5end_conserved_hypothetical_protein;_possible_periplasmic_protein_1803354..1803584_POSITIVE 400 172 138 190 156 tfor:TF3007|5end_conserved_hypothetical_protein_3227256..3227486_POSITIVE 393 130 81 82 31 tfor:TF2724|5end_anti-sigma_factor_2898193..2898423_POSITIVE 391 50 4 197 151 tfor:TF0250|5end_glycosyltransferase_Family_2_protein_279176..279406_POSITIVE 390 50 3 192 130 tfor:TF2229.1|5end_rteR_regulatory_ortholog_(with_internal_stop)_2399454..2399684_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 485 49 1 52 5 tfor:TF2631|3end_conserved_hypothetical_protein_2802088..2802238_POSITIVE 473 177 132 54 7 tfor:TF2765|3end_subtilisin-like_serine_protease_2951460..2951610_POSITIVE 468 170 121 56 5 tfor:TF0661|3end_hypothetical_protein_708257..708407_POSITIVE 466 50 5 146 106 tfor:TF0350|3end_hypothetical_protein_371101..371251_POSITIVE 444 172 131 61 15 tfor:TF1045|3end_conserved_hypothetical_protein_1108245..1108395_POSITIVE 443 50 4 43 6 tfor:TF1908|3end_possible_phosphoglycerate_mutase_2063299..2063449_POSITIVE 443 50 1 68 22 tfor:TF1687|3end_conserved_hypothetical_protein;_possible_periplasmic_protein_1803459..1803609_POSITIVE 440 60 12 58 6 tfor:TF2019|3end_dipeptidyl_peptidase_VI_2176401..2176551_POSITIVE 408 58 12 126 79 tfor:TF2774|3end_2-amino-4-hydroxy-6-hydroxymethyldihydropteridine_pyrophosphokinase_2959719..2959869_POSITIVE 403 60 11 60 18 tfor:TF0825|3end_hypothetical_protein_883850..884000_POSITIVE 386 50 5 129 78 tfor:TF1775|3end_oxidoreductase,_Gfo/Idh/MocA_family_1914618..1914768_POSITIVE 385 50 6 56 13 tfor:TF2593|3end_amino_acid_transport_protein_2764242..2764392_POSITIVE 374 41 4 151 122 tfor:TF0214|3end_DNA_recombination_and_repair_protein,_RecN_241571..241721_POSITIVE 370 60 11 79 40 tfor:TF2224|3end_CTn_excision_protein_2394968..2395118_POSITIVE 370 50 7 147 103 tfor:TF1954|3end_long-chain-fatty-acid--CoA_ligase_2106940..2107090_POSITIVE 369 50 3 61 7 tfor:TF2120|3end_holliday_junction_endonuclease_2292760..2292910_POSITIVE 369 49 4 55 11 tfor:TF0582|3end_hemolysin-related_protein,_with_CBS_domains;_possible_gliding-motility_related_protein_613263..613413_POSITIVE 367 51 11 81 40 tfor:TF1948|3end_conserved_hypothetical_protein_2096795..2096945_POSITIVE 364 60 11 71 14 tfor:TF2761|3end_thioredoxin_2945925..2946075_POSITIVE 363 50 4 144 92 tfor:TF2746|3end_hypothetical_protein_2928246..2928396_POSITIVE