Origin IGS: tgagcacttggagaacttagttttggatatagagggcttgcaagtcatggggggggacaattggcttaattattgctattgttttatatgcattaagttacacaaatacttcgaaaagaacgtgtacggtca .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tgaccgtacacgttcttttcgaagtatttgtgtaacttaatgcatataaaacaatagcaataattaagccaattgtccccccccatgacttgcaagccctctatatccaaaactaagttctccaagtgctca Mask Tandem Repeat Region ================================================ tgagcacttggagaacttagttttggatatagagggcttgcaagtcatggggggggacaattggcttaattattgctattgttttatatgcattaagttacacaaatacttcgaaaagaacgtgtacggtca Find is-nt database================================================ Query_seq: TF1682:TF1684|TF1682:TF1684:hydrolase:zinc protease:->->:1797404..1797535 132 tgagcacttggagaacttagttttggatatagagggcttgcaagtcatggggggggacaattggcttaattattgctattgttttatatgcattaagttacacaaatacttcgaaaagaacgtgtacggtca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF1682:TF1684|TF1682:TF1684:hydrolase:zinc protease:->->:1797404..1797535 132 tgagcacttggagaacttagttttggatatagagggcttgcaagtcatggggggggacaattggcttaattattgctattgttttatatgcattaagttacacaaatacttcgaaaagaacgtgtacggtca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF1682:TF1684|TF1682:TF1684:hydrolase:zinc protease:->->:1797404..1797535 132 tgagcacttggagaacttagttttggatatagagggcttgcaagtcatggggggggacaattggcttaattattgctattgttttatatgcattaagttacacaaatacttcgaaaagaacgtgtacggtca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tgagcacttggagaacttagttttggatatagagggcttgcaagtcatggggggggacaattggcttaattattgctattgttttatatgcattaagttacacaaatacttcgaaaagaacgtgtacggtca Predict ORF larger than 30AA ================================================ Protein_Len: 41 Strand: + Start: 8 End: 130 ....... M E N L V L D I E G L Q V M G G D N W L N Y C Y C F I C I K L H K Y F E K N V Y G .. tgagcacttggagaacttagttttggatatagagggcttgcaagtcatggggggggacaattggcttaattattgctattgttttatatgcattaagttacacaaatacttcgaaaagaacgtgtacggtca 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================================================ PromScan Matrix: RpoN Strand: + Score: 82 Start: 61 End: 77 ............................................................TTGGCTTAATTATTGCT....................................................... tgagcacttggagaacttagttttggatatagagggcttgcaagtcatggggggggacaattggcttaattattgctattgttttatatgcattaagttacacaaatacttcgaaaagaacgtgtacggtca Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TF1682:TF1684|TF1682:TF1684:hydrolase:zinc protease:->->:1797404..1797535 132 tgagcacttggagaacttagttttggatatagagggcttgcaagtcatggggggggacaattggcttaattattgctattgttttatatgcattaagttacacaaatacttcgaaaagaacgtgtacggtca Intra-Species Hit: Count: 1 Min: 1 Max: 132 Len: 132 Subject: tfor_TF1682_TF1684|hydrolase:zinc protease|POSITIVE:POSITIVE|[1797404,1797535]|132 HSP 1 e-value: 5.0E-55 bit: 214.0 Len: 132 Query Start:1 Query End:132 Subject Strand: POSITIVE Subject Start: 1 Subject End: 132 tgagcacttggagaacttagttttggatatagagggcttgcaagtcatnnnnnnnnacaattggcttaattattgctattgttttatatgcattaagttacacaaatacttcgaaaagaacgtgtacggtca tgagcacttggagaacttagttttggatatagagggcttgcaagtcatggggggggacaattggcttaattattgctattgttttatatgcattaagttacacaaatacttcgaaaagaacgtgtacggtca Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGAGCACUUGGAGAACUUAGUUUUGGAUAUAGAGGGCUUGCAAGUCAUGGGGGGGGACAAUUGGCUUAAUUAUUGCUAUUGUUUUAUAUGCAUUAAGUUACACAAAUACUUCGAAAAGAACGUGUACGGUCA .((.(...((...(((((((...((.((((((((.(...((((((((.....(....)...))))).......)))...).)))))))).)))))))))...)).(((((((.....))).))))..).)). (-25.91) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGACCGUACACGUUCUUUUCGAAGUAUUUGUGUAACUUAAUGCAUAUAAAACAAUAGCAAUAAUUAAGCCAAUUGUCCCCCCCCAUGACUUGCAAGCCCUCUAUAUCCAAAACUAAGUUCUCCAAGUGCUCA .((.((....)).)).....((.(((((((.(.((((((.(((.(((......))))))........((.....(((.........)))..))....................))))))..)))))))))). (-15.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 364 67 21 60 21 tfor:TF1113|5end_possible_transposase_1183767..1183997_POSITIVE 340 58 11 198 155 tfor:TF1433|5end_ribose_5-phosphate_isomerase_1517031..1517261_POSITIVE 338 65 21 177 131 tfor:TF1528|5end_malate_dehydrogenase_1633287..1633517_POSITIVE 331 69 21 184 134 tfor:TF2899|5end_conserved_hypothetical_protein_3087495..3087725_POSITIVE 326 67 32 46 1 tfor:TF1919|5end_hypothetical_protein_2070037..2070267_POSITIVE 323 67 21 66 28 tfor:TF2496|5end_butyryl-CoA_dehydrogenase,_short_chain_acyl-CoA_dehydrogenase_2670840..2671070_POSITIVE 322 76 33 212 165 tfor:TF1282|5end_tRNA_delta-2_isopentenylpyrophosphate_transferase_1366437..1366667_POSITIVE 319 79 36 79 30 tfor:TF1834|5end_3-isopropylmalate_dehydrogenase_1983161..1983391_POSITIVE 317 57 13 129 73 tfor:TF0356|5end_transposase_element_373519..373749_POSITIVE 313 65 31 226 197 tfor:TF2219|5end_two-component_system_sensor_histidine_2390844..2391074_POSITIVE 309 65 32 170 133 tfor:TF1292|5end_sensor_histidine_protein_kinase_1372567..1372797_POSITIVE 307 76 32 207 163 tfor:TF0712|5end_TPR-repeat-containing_protein_761348..761578_POSITIVE 298 67 23 139 91 tfor:TF2754|5end_hypothetical_protein_2940446..2940676_POSITIVE 298 64 21 117 82 tfor:TF2411|5end_outer_membrane_protein_2585451..2585681_POSITIVE 298 66 35 175 138 tfor:TF0931|5end_superfamily_II_DNA/RNA_helicase,_SNF2_family_970031..970261_POSITIVE 295 67 21 114 63 tfor:TF2653|5end_hypothetical_protein_2822093..2822323_POSITIVE 292 57 11 88 31 tfor:TF0865|5end_chloromuconate_cycloisomerase_915655..915885_POSITIVE 290 56 11 222 171 tfor:TF1686|5end_alginate_O-acetylation_protein_1800420..1800650_POSITIVE 290 56 11 53 2 tfor:TF1685|5end_hypothetical_protein_1800251..1800481_POSITIVE 289 63 26 109 71 tfor:TF1494|5end_cobinamide_kinase/cobinamide_phosphate_guanylyltransferase_1594016..1594246_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 340 58 11 77 34 tfor:TF1432|3end_possible_hemolysin_A_1516990..1517140_POSITIVE 311 65 24 83 47 tfor:TF0419|3end_conserved_hypothetical_protein_435794..435944_POSITIVE 304 67 23 37 1 tfor:TF2495|3end_succinate-semialdehyde_dehydrogenase_(NADP+)_2670891..2671041_POSITIVE 298 67 23 61 13 tfor:TF2753|3end_zinc_protease_2940448..2940598_POSITIVE 298 68 35 113 82 tfor:TF0880|3end_conserved_hypothetical_protein_934371..934521_POSITIVE 295 67 21 63 12 tfor:TF2652|3end_hypothetical_protein_2822122..2822272_POSITIVE 295 57 12 43 1 tfor:TF0489|3end_D-xylose-proton_symporter_513069..513219_POSITIVE 292 57 11 61 4 tfor:TF0864|3end_O-succinylbenzoate--CoA_ligase_915708..915858_POSITIVE 289 63 26 79 41 tfor:TF1493|3end_thioredoxin_family_protein_1594066..1594216_POSITIVE 288 49 2 93 42 tfor:TF0766|3end_hypothetical_protein_812256..812406_POSITIVE 288 59 32 149 120 tfor:TF0710|3end_two_component_system_histidine_kinase_761385..761535_POSITIVE 287 76 35 57 16 tfor:TF1275|3end_transcription-repair_coupling_factor_1361290..1361440_POSITIVE 284 66 23 110 57 tfor:TF1658|3end_glycosyltranferase_1774653..1774803_POSITIVE 277 68 25 118 60 tfor:TF0175|3end_hypothetical_protein_185907..186057_POSITIVE 274 64 34 141 109 tfor:TF2181|3end_conserved_hypothetical_protein_2354963..2355113_POSITIVE 269 65 25 95 49 tfor:TF1307|3end_50S_ribosomal_protein_L33_1387276..1387426_POSITIVE 265 64 30 145 119 tfor:TF1981|3end_mannose-6-phosphate_isomerase_2131944..2132094_POSITIVE 265 64 30 145 119 tfor:TF1825|3end_mannose-6-phosphate_isomerase_1974626..1974776_POSITIVE 264 66 32 66 25 tfor:TF0993|3end_hypothetical_protein_1048782..1048932_POSITIVE 263 66 33 29 1 tfor:TF0930|3end_conserved_hypothetical_protein;_possible_prophage_protein_969965..970115_POSITIVE