Origin IGS: taaccgtttgtggcggaatctctcttgcattccataacgggagaactgctctcgggccagccgtatgctctgatcggcagcttggataaaaaagctgtttgcaccgatacggaaacggtcttgagtgatta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 taatcactcaagaccgtttccgtatcggtgcaaacagcttttttatccaagctgccgatcagagcatacggctggcccgagagcagttctcccgttatggaatgcaagagagattccgccacaaacggtta Mask Tandem Repeat Region ================================================ taaccgtttgtggcggaatctctcttgcattccataacgggagaactgctctcgggccagccgtatgctctgatcggcagcttggataaaaaagctgtttgcaccgatacggaaacggtcttgagtgatta Find is-nt database================================================ Query_seq: TF1899:TF1900|TF1899:TF1900:anti-sigma factor:conserved hypothetical protein:->->:2053876..2054006 131 taaccgtttgtggcggaatctctcttgcattccataacgggagaactgctctcgggccagccgtatgctctgatcggcagcttggataaaaaagctgtttgcaccgatacggaaacggtcttgagtgatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF1899:TF1900|TF1899:TF1900:anti-sigma factor:conserved hypothetical protein:->->:2053876..2054006 131 taaccgtttgtggcggaatctctcttgcattccataacgggagaactgctctcgggccagccgtatgctctgatcggcagcttggataaaaaagctgtttgcaccgatacggaaacggtcttgagtgatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF1899:TF1900|TF1899:TF1900:anti-sigma factor:conserved hypothetical protein:->->:2053876..2054006 131 taaccgtttgtggcggaatctctcttgcattccataacgggagaactgctctcgggccagccgtatgctctgatcggcagcttggataaaaaagctgtttgcaccgatacggaaacggtcttgagtgatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taaccgtttgtggcggaatctctcttgcattccataacgggagaactgctctcgggccagccgtatgctctgatcggcagcttggataaaaaagctgtttgcaccgatacggaaacggtcttgagtgatta Predict ORF larger than 30AA ================================================ Protein_Len: 40 Strand: + Start: 10 End: 129 ......... M A E S L L H S I T G E L L S G Q P Y A L I G S L D K K A V C T D T E T V L S D .. Protein_Len: 34 Strand: - Start: 3 End: 104 .. G N T A S D R K C E M V P S S S E P W G Y A R I P L K S L F A T Q M ........................... Protein_Len: 43 Strand: - Start: 1 End: 129 L R K H R F R E Q M G Y R S F Q E R A L R I S Q D A A Q I F F S N A G I R F R D Q T M .. taaccgtttgtggcggaatctctcttgcattccataacgggagaactgctctcgggccagccgtatgctctgatcggcagcttggataaaaaagctgtttgcaccgatacggaaacggtcttgagtgatta 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================================================ taaccgtttgtggcggaatctctcttgcattccataacgggagaactgctctcgggccagccgtatgctctgatcggcagcttggataaaaaagctgtttgcaccgatacggaaacggtcttgagtgatta Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 49 HP_score: -3.6 Tail_Score: -3.32844 Start: 38 End: 54 Full_Region: agcatacggctggcc cgagag cagtt ctcccg ttatggaatgcaaga .....................................cgagagcagttctcccg............................................................................. Find igs database================================================ Query_seq: TF1899:TF1900|TF1899:TF1900:anti-sigma factor:conserved hypothetical protein:->->:2053876..2054006 131 taaccgtttgtggcggaatctctcttgcattccataacgggagaactgctctcgggccagccgtatgctctgatcggcagcttggataaaaaagctgtttgcaccgatacggaaacggtcttgagtgatta Intra-Species Hit: Count: 1 Min: 1 Max: 131 Len: 131 Subject: tfor_TF1899_TF1900|anti-sigma factor:conserved hypothetical protein|POSITIVE:POSITIVE|[2053876,2054006]|131 HSP 1 e-value: 1.0E-68 bit: 260.0 Len: 131 Query Start:1 Query End:131 Subject Strand: POSITIVE Subject Start: 1 Subject End: 131 taaccgtttgtggcggaatctctcttgcattccataacgggagaactgctctcgggccagccgtatgctctgatcggcagcttggataaaaaagctgtttgcaccgatacggaaacggtcttgagtgatta taaccgtttgtggcggaatctctcttgcattccataacgggagaactgctctcgggccagccgtatgctctgatcggcagcttggataaaaaagctgtttgcaccgatacggaaacggtcttgagtgatta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAACCGUUUGUGGCGGAAUCUCUCUUGCAUUCCAUAACGGGAGAACUGCUCUCGGGCCAGCCGUAUGCUCUGAUCGGCAGCUUGGAUAAAAAAGCUGUUUGCACCGAUACGGAAACGGUCUUGAGUGAUUA ..(((((((.((((((((((......).)))))....((((((.....)))))).)))).((((((.(..((...((((((((........))))))))..))..))))))))))))))............ (-41.20) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAUCACUCAAGACCGUUUCCGUAUCGGUGCAAACAGCUUUUUUAUCCAAGCUGCCGAUCAGAGCAUACGGCUGGCCCGAGAGCAGUUCUCCCGUUAUGGAAUGCAAGAGAGAUUCCGCCACAAACGGUUA ...........(((((((((((((.(((.(..(((.((((((....(((....((((...........)))))))...)))))).)))..)))).))))))..((..((....))..))....))))))). (-32.10) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 436 80 38 140 99 tfor:TF1465|5end_modulator_of_DNA_gyrase_1554148..1554378_POSITIVE 423 86 41 71 14 tfor:TF2366|5end_conserved_hypothetical_protein_2531297..2531527_POSITIVE 418 80 38 193 147 tfor:TF2160|5end_magnesium_chelatase,_subunit_I_2335974..2336204_POSITIVE 397 58 12 166 128 tfor:TF1586|5end_hypothetical_protein_1690971..1691201_POSITIVE 395 90 45 229 174 tfor:TF2595|5end_conserved_hypothetical_protein_2765084..2765314_POSITIVE 393 120 72 222 181 tfor:TF3112|5end_Na+/H+_anitporter_3346775..3347005_POSITIVE 393 120 72 48 7 tfor:TF3111|5end_hypothetical_protein_3346601..3346831_POSITIVE 393 79 36 76 22 tfor:TF0697|5end_glycerol-3-phosphate_cytidyltransferase_740667..740897_POSITIVE 392 85 49 184 144 tfor:TF1363|5end_conserved_hypothetical_protein_1444083..1444313_POSITIVE 389 89 46 210 163 tfor:TF3072|5end_conserved_hypothetical_protein_3295302..3295532_POSITIVE 386 80 32 202 167 tfor:TF0474|5end_outer_membrane_efflux_protein_492104..492334_POSITIVE 379 80 31 84 11 tfor:TF2932|5end_capsule_biosynthesis_protein_3135514..3135744_POSITIVE 377 55 14 168 124 tfor:TF2712|5end_glycosyltransferase_2885918..2886148_POSITIVE 376 79 38 179 134 tfor:TF0759|5end_heat_shock_protein_15,_RNA-binding_domain_S4_805870..806100_POSITIVE 375 81 48 71 40 tfor:TF1961|5end_isoprenoid_biosynthesis_related_protein_2111420..2111650_POSITIVE 374 84 46 223 177 tfor:TF2430|5end_hypothetical_protein_2612660..2612890_POSITIVE 373 99 53 161 107 tfor:TF0142|5end_subtilisin-like_serine_proteinase_149740..149970_POSITIVE 372 80 38 58 24 tfor:TF2152|5end_uronate_isomerase_2326575..2326805_POSITIVE 371 84 44 112 67 tfor:TF2986|5end_conserved_hypothetical_protein;_possible_glycosyltransferase_3201818..3202048_POSITIVE 370 86 46 198 142 tfor:TF2520|5end_conserved_hypothetical_protein_2698917..2699147_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 406 79 38 141 95 tfor:TF0012|3end_conserved_hypothetical_protein_6641..6791_POSITIVE 393 79 36 70 16 tfor:TF0696|3end_3-oxoacyl-(acyl-carrier-protein)_reductase_740741..740891_POSITIVE 392 85 49 80 40 tfor:TF1362|3end_hypothetical_protein_1444059..1444209_POSITIVE 379 80 31 74 1 tfor:TF2931|3end_3-deoxy-D-manno-2-octulosonic_acid_(Kdo_transferase)_3135584..3135734_POSITIVE 372 80 38 58 24 tfor:TF2150|3end_Na+/phosphate_symporter_2326655..2326805_POSITIVE 369 84 47 32 1 tfor:TF1464|3end_conserved_hypothetical_protein_1554116..1554266_POSITIVE 368 79 39 142 99 tfor:TF1351|3end_conserved_hypothetical_protein_1432050..1432200_POSITIVE 368 68 21 135 65 tfor:TF1282|3end_tRNA_delta-2_isopentenylpyrophosphate_transferase_1367431..1367581_POSITIVE 366 86 46 66 19 tfor:TF1934|3end_hypothetical_protein_2084079..2084229_POSITIVE 357 79 38 63 4 tfor:TF3107|3end_hypothetical_protein_3338736..3338886_POSITIVE 355 78 32 63 20 tfor:TF1796|3end_ABC_transporter,_ATP-binding_protein_1937216..1937366_POSITIVE 352 69 23 144 81 tfor:TF2125|3end_conserved_hypothetical_protein_2302465..2302615_POSITIVE 347 99 51 106 54 tfor:TF0880|3end_conserved_hypothetical_protein_934371..934521_POSITIVE 345 86 43 66 9 tfor:TF1852|3end_prtQ_protein_2006546..2006696_POSITIVE 341 82 46 149 111 tfor:TF0141|3end_exodeoxyribonuclease_VII,_large_subunit_149830..149980_POSITIVE 340 120 73 60 12 tfor:TF2753|3end_zinc_protease_2940448..2940598_POSITIVE 340 86 46 51 11 tfor:TF1909|3end_cobalamin_(5`-phosphate)_synthase_2064075..2064225_POSITIVE 339 98 51 135 83 tfor:TF2921|3end_hypothetical_protein_3118790..3118940_POSITIVE 339 90 47 60 23 tfor:TF1468|3end_beta-galactosidase_1561251..1561401_POSITIVE 339 85 48 131 94 tfor:TF0027|3end_conserved_hypothetical_protein_24199..24349_POSITIVE