Origin IGS: gtcttttttatcatttaaatttcggatgcaaagttagaagcaccgatattacggcgcaatccccaattctatggatttttttggtcgttttatccccaataattgggatgttttctcaatgttcttccttaagaaaaaaagagagaagatgatgaaacaacatcccctctctttcatgtttttgaaaaagttaaactta .........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 taagtttaactttttcaaaaacatgaaagagaggggatgttgtttcatcatcttctctctttttttcttaaggaagaacattgagaaaacatcccaattattggggataaaacgaccaaaaaaatccatagaattggggattgcgccgtaatatcggtgcttctaactttgcatccgaaatttaaatgataaaaaagac Mask Tandem Repeat Region ================================================ gtcttttttatcatttaaatttcggatgcaaagttagaagcaccgatattacggcgcaatccccaattctatggatttttttggtcgttttatccccaataattgggatgttttctcaatgttcttccttaagaaaaaaagagagaagatgatgaaacaacatcccctctctttcatgtttttgaaaaagttaaactta Find is-nt database================================================ Query_seq: TF3068:TF3069|TF3068:TF3069:flavodoxin A:hypothetical protein:->->:3293444..3293642 199 gtcttttttatcatttaaatttcggatgcaaagttagaagcaccgatattacggcgcaatccccaattctatggatttttttggtcgttttatccccaataattgggatgttttctcaatgttcttccttaagaaaaaaagagagaagatgatgaaacaacatcccctctctttcatgtttttgaaaaagttaaactta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF3068:TF3069|TF3068:TF3069:flavodoxin A:hypothetical protein:->->:3293444..3293642 199 gtcttttttatcatttaaatttcggatgcaaagttagaagcaccgatattacggcgcaatccccaattctatggatttttttggtcgttttatccccaataattgggatgttttctcaatgttcttccttaagaaaaaaagagagaagatgatgaaacaacatcccctctctttcatgtttttgaaaaagttaaactta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF3068:TF3069|TF3068:TF3069:flavodoxin A:hypothetical protein:->->:3293444..3293642 199 gtcttttttatcatttaaatttcggatgcaaagttagaagcaccgatattacggcgcaatccccaattctatggatttttttggtcgttttatccccaataattgggatgttttctcaatgttcttccttaagaaaaaaagagagaagatgatgaaacaacatcccctctctttcatgtttttgaaaaagttaaactta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gtcttttttatcatttaaatttcggatgcaaagttagaagcaccgatattacggcgcaatccccaattctatggatttttttggtcgttttatccccaataattgggatgttttctcaatgttcttccttaagaaaaaaagagagaagatgatgaaacaacatcccctctctttcatgtttttgaaaaagttaaactta Predict ORF larger than 30AA ================================================ Protein_Len: 34 Strand: + Start: 48 End: 149 ............................................... M T A Q S P I L W I F L V V L S P I I G M F S Q C S S L R K K E R R .................................................. Protein_Len: 47 Strand: + Start: 59 End: 199 .......................................................... M P N S M D F F G R F I P N N W D V F S M F F L K K K R E K M M K Q H P L S F M F L K K L N L Protein_Len: 42 Strand: - Start: 52 End: 177 ................................................... P A I G L E I S K K P R K I G L L Q S T K E I N K R L F F L S F I I F C C G R E K M ...................... Protein_Len: 32 Strand: - Start: 14 End: 109 ............. K F K P H L T L L V S I V A C D G I R H I K K T T K D G I I P M .......................................................................................... gtcttttttatcatttaaatttcggatgcaaagttagaagcaccgatattacggcgcaatccccaattctatggatttttttggtcgttttatccccaataattgggatgttttctcaatgttcttccttaagaaaaaaagagagaagatgatgaaacaacatcccctctctttcatgtttttgaaaaagttaaactta 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================================================ gtcttttttatcatttaaatttcggatgcaaagttagaagcaccgatattacggcgcaatccccaattctatggatttttttggtcgttttatccccaataattgggatgttttctcaatgttcttccttaagaaaaaaagagagaagatgatgaaacaacatcccctctctttcatgtttttgaaaaagttaaactta Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 48 HP_score: -3.0 Tail_Score: -3.49048 Start: 103 End: 119 Full_Region: TTTTATCCCCAATAA TTGGGA TGTTT TCTCAA TGTTCTTCCTTAAGA ......................................................................................................TTGGGATGTTTTCTCAA................................................................................ TransTerm Strand: + Conf: 70 HP_score: -6.8 Tail_Score: -4.13748 Start: 141 End: 171 Full_Region: TCCTTAAGAAAAAAA GAGAGAAGATGATG AAA CAACATCCCCTCTC TTTCATGTTTTTGAA ............................................................................................................................................GAGAGAAGATGATGAAACAACATCCCCTCTC............................ Find igs database================================================ Query_seq: TF3068:TF3069|TF3068:TF3069:flavodoxin A:hypothetical protein:->->:3293444..3293642 199 gtcttttttatcatttaaatttcggatgcaaagttagaagcaccgatattacggcgcaatccccaattctatggatttttttggtcgttttatccccaataattgggatgttttctcaatgttcttccttaagaaaaaaagagagaagatgatgaaacaacatcccctctctttcatgtttttgaaaaagttaaactta Intra-Species Hit: Count: 1 Min: 1 Max: 199 Len: 199 Subject: tfor_TF3068_TF3069|flavodoxin A:hypothetical protein|POSITIVE:POSITIVE|[3293444,3293642]|199 HSP 1 e-value: 5.0E-84 bit: 311.0 Len: 199 Query Start:1 Query End:199 Subject Strand: POSITIVE Subject Start: 1 Subject End: 199 gtcttttttatcatttaaatttcggatgcaaagttagaagcaccgatattacggcgcaatccccaattctatggannnnnnnggtcgttttatccccaataattgggatgttttctcaatgttcttccttaagnnnnnnngagagaagatgatgaaacaacatcccctctctttcatgtttttgaaaaagttaaactta gtcttttttatcatttaaatttcggatgcaaagttagaagcaccgatattacggcgcaatccccaattctatggatttttttggtcgttttatccccaataattgggatgttttctcaatgttcttccttaagaaaaaaagagagaagatgatgaaacaacatcccctctctttcatgtttttgaaaaagttaaactta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUCUUUUUUAUCAUUUAAAUUUCGGAUGCAAAGUUAGAAGCACCGAUAUUACGGCGCAAUCCCCAAUUCUAUGGAUUUUUUUGGUCGUUUUAUCCCCAAUAAUUGGGAUGUUUUCUCAAUGUUCUUCCUUAAGAAAAAAAGAGAGAAGAUGAUGAAACAACAUCCCCUCUCUUUCAUGUUUUUGAAAAAGUUAAACUUA .............(((((.(((((((.((((((..((((.....((((..(((((.(((...(((......)))......))))))))..)))).......(((((((.....))))))).))))..))).......((((((((..((((.((...)).))))..))))))))..))).)))))))...))))).... (-42.50) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAGUUUAACUUUUUCAAAAACAUGAAAGAGAGGGGAUGUUGUUUCAUCAUCUUCUCUCUUUUUUUCUUAAGGAAGAACAUUGAGAAAACAUCCCAAUUAUUGGGGAUAAAACGACCAAAAAAAUCCAUAGAAUUGGGGAUUGCGCCGUAAUAUCGGUGCUUCUAACUUUGCAUCCGAAAUUUAAAUGAUAAAAAAGAC (((((((...((((((((......(((((((((((((((.((...)).))))))))))))))).(((((....)))))..))))))))...((((((((.....((((...............))))....))))))))...((((((......)))))).................)))))))............... (-50.86) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 330 53 12 41 4 tfor:TF0238|5end_outer_membrane_protein_266871..267101_POSITIVE 323 86 42 69 20 tfor:TF0758|5end_peptidyl-tRNA_hydrolase_805307..805537_POSITIVE 321 97 52 100 47 tfor:TF0777|5end_1,4-dihydroxy-2-naphthoate_octaprenyltransferase_826098..826328_POSITIVE 317 175 135 231 191 tfor:TF1260|5end_chaperone_protein_DnaJ_1345325..1345555_POSITIVE 316 66 23 202 156 tfor:TF2770|5end_conserved_hypothetical_protein_2956308..2956538_POSITIVE 303 90 51 174 126 tfor:TF2804|5end_conserved_hypothetical_protein_2993494..2993724_POSITIVE 299 98 53 188 146 tfor:TF0599|5end_hypothetical_protein_629835..630065_POSITIVE 291 54 13 140 104 tfor:TF1885|5end_conserved_hypothetical_protein_2037307..2037537_POSITIVE 285 90 41 78 32 tfor:TF2575|5end_methionine_aminopeptidase_2745126..2745356_POSITIVE 283 129 82 177 113 tfor:TF2241|5end_ATP-dependent_DNA_helicase_2415401..2415631_POSITIVE 281 117 71 145 92 tfor:TF1556|5end_hypothetical_protein_1662404..1662634_POSITIVE 280 100 51 102 23 tfor:TF2396|5end_dimethyladenosine_transferase_2567725..2567955_POSITIVE 277 64 23 214 169 tfor:TF2704|5end_ribonuclease_HII_2876242..2876472_POSITIVE 275 84 42 227 192 tfor:TF1829|5end_2-isopropylmalate_synthase_1977365..1977595_POSITIVE 274 64 24 84 44 tfor:TF0187|5end_ferredoxin_202151..202381_POSITIVE 273 69 21 60 19 tfor:TF0780|5end_alpha-L-arabinofuranosidase,_precursor_A_831944..832174_POSITIVE 272 109 62 214 170 tfor:TF3043|5end_conserved_hypothetical_protein_3271925..3272155_POSITIVE 271 97 51 49 11 tfor:TF1174|5end_ABC_transporter,_permease_component_1256584..1256814_POSITIVE 270 98 54 165 121 tfor:TF2265|5end_transfer_region-related_protein,_TraP;_DNA_primase_involved_in_conjugation_2433474..2433704_POSITIVE 270 94 52 211 173 tfor:TF1300|5end_conserved_hypothetical_protein_1382389..1382619_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 321 97 52 95 42 tfor:TF0776|3end_ABC_transporter,_permease_component_826173..826323_POSITIVE 303 90 51 67 19 tfor:TF2803|3end_dehydrogenase,_possible_NADH-dependent_dehydrogenase_2993467..2993617_POSITIVE 285 90 41 72 26 tfor:TF2574|3end_preprotein_translocase_SecY_2745200..2745350_POSITIVE 283 129 82 113 49 tfor:TF2240|3end__tetracycline_resistance_element_mobilization_regulatory_protein_2415417..2415567_POSITIVE 281 117 71 130 77 tfor:TF1555|3end_hypothetical_protein_1662469..1662619_POSITIVE 272 61 22 120 73 tfor:TF1049|3end_cobyrinic_acid_a,c-diamide_synthase_1111539..1111689_POSITIVE 267 130 81 58 3 tfor:TF2497|3end_electron_transfer_flavoprotein,_beta-subunit_2672854..2673004_POSITIVE 265 97 53 36 2 tfor:TF1173|3end_ABC_transporter,_permease_component_1256651..1256801_POSITIVE 261 95 52 133 100 tfor:TF0439|3end_Na+-transporting_NADH:ubiquinone_oxidoreductase,_subunit_1_463689..463839_POSITIVE 260 107 69 125 89 tfor:TF0545|3end_glucose-inhibited_division_protein_B_576453..576603_POSITIVE 256 99 51 95 32 tfor:TF1076|3end_possible_glycerol_kinase_1145681..1145831_POSITIVE 254 64 24 109 70 tfor:TF1452|3end_conserved_hypothetical_protein;_possible_transglutaminase-like_enzyme_1539657..1539807_POSITIVE 253 66 25 66 20 tfor:TF1474|3end_6-phosphogluconolactonase_1568123..1568273_POSITIVE 252 57 23 71 30 tfor:TF3107|3end_hypothetical_protein_3338736..3338886_POSITIVE 252 98 51 65 3 tfor:TF2501|3end_DNA_mismatch_repair_protein_2678183..2678333_POSITIVE 251 125 83 97 65 tfor:TF1868|3end_conserved_hypothetical_protein;_possible_transposase_2023043..2023193_POSITIVE 251 168 133 142 106 tfor:TF1175|3end_membrane-fusion_protein_1259470..1259620_POSITIVE 250 87 51 151 110 tfor:TF3085|3end_hypothetical_protein_3319003..3319153_POSITIVE 250 87 51 151 110 tfor:TF3083|3end_hypothetical_protein_3317699..3317849_POSITIVE 249 65 21 141 91 tfor:TF3099|3end_conserved_hypothetical_protein_3331107..3331257_POSITIVE