Origin IGS: taaatatagaaaaaggcggtgtgtcataacgggcgaactgcttcgttgcttacggaatgcgtgctcggttacataccttagtatactccctcgctctcatccttaattccttgcatttcacccatgcattgcgttttgacacaccctcgcaaaagattttttcttctcacacttta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 taaagtgtgagaagaaaaaatcttttgcgagggtgtgtcaaaacgcaatgcatgggtgaaatgcaaggaattaaggatgagagcgagggagtatactaaggtatgtaaccgagcacgcattccgtaagcaacgaagcagttcgcccgttatgacacaccgcctttttctatattta Mask Tandem Repeat Region ================================================ taaatatagaaaaaggcggtgtgtcataacgggcgaactgcttcgttgcttacggaatgcgtgctcggttacataccttagtatactccctcgctctcatccttaattccttgcatttcacccatgcattgcgttttgacacaccctcgcaaaagattttttcttctcacacttta Find is-nt database================================================ Query_seq: TF0795:TF0797|TF0795:TF0797:hypothetical protein:conserved hypothetical protein:->->:853260..853435 176 taaatatagaaaaaggcggtgtgtcataacgggcgaactgcttcgttgcttacggaatgcgtgctcggttacataccttagtatactccctcgctctcatccttaattccttgcatttcacccatgcattgcgttttgacacaccctcgcaaaagattttttcttctcacacttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF0795:TF0797|TF0795:TF0797:hypothetical protein:conserved hypothetical protein:->->:853260..853435 176 taaatatagaaaaaggcggtgtgtcataacgggcgaactgcttcgttgcttacggaatgcgtgctcggttacataccttagtatactccctcgctctcatccttaattccttgcatttcacccatgcattgcgttttgacacaccctcgcaaaagattttttcttctcacacttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF0795:TF0797|TF0795:TF0797:hypothetical protein:conserved hypothetical protein:->->:853260..853435 176 taaatatagaaaaaggcggtgtgtcataacgggcgaactgcttcgttgcttacggaatgcgtgctcggttacataccttagtatactccctcgctctcatccttaattccttgcatttcacccatgcattgcgttttgacacaccctcgcaaaagattttttcttctcacacttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taaatatagaaaaaggcggtgtgtcataacgggcgaactgcttcgttgcttacggaatgcgtgctcggttacataccttagtatactccctcgctctcatccttaattccttgcatttcacccatgcattgcgttttgacacaccctcgcaaaagattttttcttctcacacttta Predict ORF larger than 30AA ================================================ Protein_Len: 40 Strand: + Start: 57 End: 176 ........................................................ M R A R L H T L V Y S L A L I L N S L H F T H A L R F D T P S Q K I F S S H T L Protein_Len: 30 Strand: - Start: 81 End: 170 ................................................................................ Y V G E S E D K I G Q M E G M C Q T K V C G R L L N K R R M ...... Protein_Len: 35 Strand: - Start: 53 End: 157 .................................................... P I R A R N C V K T Y E R A R M R L E K C K V W A N R K S V G E C F M ................... taaatatagaaaaaggcggtgtgtcataacgggcgaactgcttcgttgcttacggaatgcgtgctcggttacataccttagtatactccctcgctctcatccttaattccttgcatttcacccatgcattgcgttttgacacaccctcgcaaaagattttttcttctcacacttta 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================================================ taaatatagaaaaaggcggtgtgtcataacgggcgaactgcttcgttgcttacggaatgcgtgctcggttacataccttagtatactccctcgctctcatccttaattccttgcatttcacccatgcattgcgttttgacacaccctcgcaaaagattttttcttctcacacttta Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TF0795:TF0797|TF0795:TF0797:hypothetical protein:conserved hypothetical protein:->->:853260..853435 176 taaatatagaaaaaggcggtgtgtcataacgggcgaactgcttcgttgcttacggaatgcgtgctcggttacataccttagtatactccctcgctctcatccttaattccttgcatttcacccatgcattgcgttttgacacaccctcgcaaaagattttttcttctcacacttta Intra-Species Hit: Count: 3 Min: 1 Max: 176 Len: 176 Subject: tfor_TF0795_TF0797|hypothetical protein:conserved hypothetical protein|POSITIVE:POSITIVE|[853260,853435]|176 HSP 1 e-value: 2.0E-95 bit: 349.0 Len: 176 Query Start:1 Query End:176 Subject Strand: POSITIVE Subject Start: 1 Subject End: 176 taaatatagaaaaaggcggtgtgtcataacgggcgaactgcttcgttgcttacggaatgcgtgctcggttacataccttagtatactccctcgctctcatccttaattccttgcatttcacccatgcattgcgttttgacacaccctcgcaaaagattttttcttctcacacttta taaatatagaaaaaggcggtgtgtcataacgggcgaactgcttcgttgcttacggaatgcgtgctcggttacataccttagtatactccctcgctctcatccttaattccttgcatttcacccatgcattgcgttttgacacaccctcgcaaaagattttttcttctcacacttta Subject: tfor_TF0145_TF0146|glutamine synthetase:glutamine-dependent NAD(+) synthetase|POSITIVE:POSITIVE|[154779,154994]|216 HSP 1 e-value: 1.0E-28 bit: 127.0 Len: 108 Query Start:15 Query End:122 Subject Strand: POSITIVE Subject Start: 11 Subject End: 118 ..............ggcggtgtgtcataacgggcgaactgcttcgttgcttacggaatgcgtgctcggttacataccttagtatactccctcgctctcatccttaattccttgcatttcacc...................................................... ..............ggcggtgtgtcataacgggcgaactgcttcgttgcttgcggaatgcaagctcggtcacatacgttagtatgctccctcgttcgcatccttagcgccttgcatttcacc...................................................... Subject: tfor_TF0475_TF0476|possible transcriptional regulator, AraC family:conserved hypothetical protein|POSITIVE:POSITIVE|[494886,495083]|198 HSP 1 e-value: 3.0E-11 bit: 69.9 Len: 103 Query Start:25 Query End:127 Subject Strand: POSITIVE Subject Start: 14 Subject End: 116 ........................cataacgggcgaactgcttcgttgcttacggaatgcgtgctcggttacataccttagtatactccctcgctctcatccttaattccttgcatttcacccatgc................................................. ........................cataacgggagaactgcttcgtttcctgctgaatgtaaactcggtcatatacgtttgtatactccctcgctctcatccttagcgtcttgcatttcacccatgc................................................. Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAAUAUAGAAAAAGGCGGUGUGUCAUAACGGGCGAACUGCUUCGUUGCUUACGGAAUGCGUGCUCGGUUACAUACCUUAGUAUACUCCCUCGCUCUCAUCCUUAAUUCCUUGCAUUUCACCCAUGCAUUGCGUUUUGACACACCCUCGCAAAAGAUUUUUUCUUCUCACACUUUA .......((((((((..(((((((((.((((.((((...((......))....(((..(..((((.(((.....)))..))))..)))).)))).................(((((.......)))))...)))).))))))))).((......))))))))))............ (-40.30) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAAGUGUGAGAAGAAAAAAUCUUUUGCGAGGGUGUGUCAAAACGCAAUGCAUGGGUGAAAUGCAAGGAAUUAAGGAUGAGAGCGAGGGAGUAUACUAAGGUAUGUAACCGAGCACGCAUUCCGUAAGCAACGAAGCAGUUCGCCCGUUAUGACACACCGCCUUUUUCUAUAUUUA ..((((((.(((((((....((......)).(((((((((....((...))..(((((((.(((..........(((((.(.((..((..((((((....))))))..))..)).).)))))(((.....)))..))).)))))))....)))))))))...))))))))))))). (-53.20) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 835 69 21 222 174 tfor:TF0663|5end_conserved_hypothetical_protein_708450..708680_POSITIVE 835 69 21 88 40 tfor:TF0662|5end_hypothetical_protein_708316..708546_POSITIVE 763 100 53 206 159 tfor:TF0984|5end_possible_mucin-desulfating_sulfatase_(MdsC_protein)_1040259..1040489_POSITIVE 450 42 15 229 202 tfor:TF1586|5end_hypothetical_protein_1690971..1691201_POSITIVE 421 150 104 46 1 tfor:TF2671|5end_dipeptidyl_peptidase_IV_(DPP_IV)_N-terminal_region_2843918..2844148_POSITIVE 384 148 120 158 129 tfor:TF0187|5end_ferredoxin_202151..202381_POSITIVE 382 130 86 77 32 tfor:TF2724|5end_anti-sigma_factor_2898193..2898423_POSITIVE 381 68 22 105 55 tfor:TF0719|5end_hypothetical_protein_769798..770028_POSITIVE 376 151 119 207 171 tfor:TF2593|5end_amino_acid_transport_protein_2762882..2763112_POSITIVE 375 67 28 55 5 tfor:TF1032|5end_possible_internalin-related_protein_1091296..1091526_POSITIVE 368 66 21 203 144 tfor:TF0001|5end_hypothetical_protein_-116..114_POSITIVE 365 53 12 155 113 tfor:TF1505|5end_conserved_hypothetical_protein_1610773..1611003_POSITIVE 365 69 25 208 156 tfor:TF0620|5end_phosphoribosylaminoimidazole-succinocarboxamide_synthase_654711..654941_POSITIVE 364 68 21 176 123 tfor:TF2835|5end_stationary-phase_survival_protein_SurE_3025113..3025343_POSITIVE 361 77 32 208 164 tfor:TF2775|5end_conserved_hypothetical_protein;_possible_mucoidy_inhibitor-related_protein_2959668..2959898_POSITIVE 360 60 15 212 158 tfor:TF1973|5end_propionyl-CoA_carboxylase,_beta_subunit_2119360..2119590_POSITIVE 359 60 16 55 6 tfor:TF2020|5end_muconate_cycloisomerase_2176321..2176551_POSITIVE 356 68 31 164 116 tfor:TF0962|5end_possible_amidohydrolase_1011593..1011823_POSITIVE 356 69 30 51 18 tfor:TF0881|5end_conserved_hypothetical_protein_934459..934689_POSITIVE 355 59 15 198 149 tfor:TF3019|5end_tRNA_and_rRNA_cytosine-C5-methylase_3242164..3242394_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 414 170 121 65 22 tfor:TF2765|3end_subtilisin-like_serine_protease_2951460..2951610_POSITIVE 413 148 121 58 30 tfor:TF0661|3end_hypothetical_protein_708257..708407_POSITIVE 376 151 119 52 16 tfor:TF2592|3end_conserved_hypothetical_protein_2762807..2762957_POSITIVE 372 55 11 81 35 tfor:TF1948|3end_conserved_hypothetical_protein_2096795..2096945_POSITIVE 364 60 12 57 15 tfor:TF0825|3end_hypothetical_protein_883850..884000_POSITIVE 359 60 16 55 6 tfor:TF2019|3end_dipeptidyl_peptidase_VI_2176401..2176551_POSITIVE 351 148 121 61 34 tfor:TF1045|3end_conserved_hypothetical_protein_1108245..1108395_POSITIVE 349 68 21 145 95 tfor:TF2206|3end_conserved_hypothetical_protein;_possible_sugar_phosphate_isomerase/epimerase_2380987..2381137_POSITIVE 347 69 22 80 16 tfor:TF0655|3end_outer_membrane_protein_701907..702057_POSITIVE 344 57 17 65 26 tfor:TF3029|3end_membrane_peptidase_3253758..3253908_POSITIVE 343 68 24 67 22 tfor:TF1930|3end_two-component_response_regulator_2078203..2078353_POSITIVE 342 58 17 73 33 tfor:TF1586|3end_hypothetical_protein_1700338..1700488_POSITIVE 340 127 83 151 110 tfor:TF1276|3end_acyl-CoA_dehydrogenase_(short_chain_coenzyme_A_dehydrogenase)_1363080..1363230_POSITIVE 339 59 15 61 14 tfor:TF2761|3end_thioredoxin_2945925..2946075_POSITIVE 336 68 21 132 85 tfor:TF2774|3end_2-amino-4-hydroxy-6-hydroxymethyldihydropteridine_pyrophosphokinase_2959719..2959869_POSITIVE 332 60 14 89 31 tfor:TF1167|3end_hypothetical_protein_1248932..1249082_POSITIVE 329 128 88 119 81 tfor:TF2654|3end_arginyl-tRNA_synthetase_2824559..2824709_POSITIVE 329 95 53 117 66 tfor:TF1914|3end_conserved_hypothetical_protein_2067656..2067806_POSITIVE 328 170 121 105 37 tfor:TF1997|3end_ROK_family_transcriptional_regulator_2152686..2152836_POSITIVE 327 66 25 69 15 tfor:TF0692|3end_conserved_hypothetical_protein_736992..737142_POSITIVE