Origin IGS: tgacaatgctctatctgacgattgttttgttttatgattcatatcgtcgtcttatcctctcaaaaaaagaaatcccggaaatgcactgcacgtccgagactttttcagaagaaagtaattgctctaatcgatgcaagccctctcttttcctta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 taaggaaaagagagggcttgcatcgattagagcaattactttcttctgaaaaagtctcggacgtgcagtgcatttccgggatttctttttttgagaggataagacgacgatatgaatcataaaacaaaacaatcgtcagatagagcattgtca Mask Tandem Repeat Region ================================================ tgacaatgctctatctgacgattgttttgttttatgattcatatcgtcgtcttatcctctcaaaaaaagaaatcccggaaatgcactgcacgtccgagactttttcagaagaaagtaattgctctaatcgatgcaagccctctcttttcctta Find is-nt database================================================ Query_seq: TF1448:TF1449|TF1448:TF1449:possible competence protein:RNA polymerase sigma factor, RpoD:->->:1533111..1533263 153 tgacaatgctctatctgacgattgttttgttttatgattcatatcgtcgtcttatcctctcaaaaaaagaaatcccggaaatgcactgcacgtccgagactttttcagaagaaagtaattgctctaatcgatgcaagccctctcttttcctta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF1448:TF1449|TF1448:TF1449:possible competence protein:RNA polymerase sigma factor, RpoD:->->:1533111..1533263 153 tgacaatgctctatctgacgattgttttgttttatgattcatatcgtcgtcttatcctctcaaaaaaagaaatcccggaaatgcactgcacgtccgagactttttcagaagaaagtaattgctctaatcgatgcaagccctctcttttcctta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF1448:TF1449|TF1448:TF1449:possible competence protein:RNA polymerase sigma factor, RpoD:->->:1533111..1533263 153 tgacaatgctctatctgacgattgttttgttttatgattcatatcgtcgtcttatcctctcaaaaaaagaaatcccggaaatgcactgcacgtccgagactttttcagaagaaagtaattgctctaatcgatgcaagccctctcttttcctta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tgacaatgctctatctgacgattgttttgttttatgattcatatcgtcgtcttatcctctcaaaaaaagaaatcccggaaatgcactgcacgtccgagactttttcagaagaaagtaattgctctaatcgatgcaagccctctcttttcctta Predict ORF larger than 30AA ================================================ Protein_Len: 49 Strand: + Start: 6 End: 152 ..... M L Y L T I V L F Y D S Y R R L I L S K K E I P E M H C T S E T F S E E S N C S N R C K P S L F L . Protein_Len: 44 Strand: + Start: 22 End: 153 ..................... M F C F M I H I V V L S S Q K K K S R K C T A R P R L F Q K K V I A L I D A S P L F S L Protein_Len: 34 Strand: - Start: 35 End: 136 .................................. S E Y R R R I R E F F S I G S I C Q V D S V K E S S L L Q E L R H M ................. tgacaatgctctatctgacgattgttttgttttatgattcatatcgtcgtcttatcctctcaaaaaaagaaatcccggaaatgcactgcacgtccgagactttttcagaagaaagtaattgctctaatcgatgcaagccctctcttttcctta 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================================================ tgacaatgctctatctgacgattgttttgttttatgattcatatcgtcgtcttatcctctcaaaaaaagaaatcccggaaatgcactgcacgtccgagactttttcagaagaaagtaattgctctaatcgatgcaagccctctcttttcctta Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 91 HP_score: -6.4 Tail_Score: -5.40474 Start: 69 End: 103 Full_Region: ttactttcttctgaa aaagtctcggacgtgc agt gcatttccgggatttc tttttttgagaggat ....................................................................aaagtctcggacgtgcagtgcatttccgggatttc.................................................. TransTerm Strand: - Conf: 100 HP_score: -9.4 Tail_Score: -5.20328 Start: 73 End: 99 Full_Region: tttcttctgaaaaag tctcggacgtgc agt gcatttccggga tttctttttttgaga ........................................................................tctcggacgtgcagtgcatttccggga...................................................... Find igs database================================================ Query_seq: TF1448:TF1449|TF1448:TF1449:possible competence protein:RNA polymerase sigma factor, RpoD:->->:1533111..1533263 153 tgacaatgctctatctgacgattgttttgttttatgattcatatcgtcgtcttatcctctcaaaaaaagaaatcccggaaatgcactgcacgtccgagactttttcagaagaaagtaattgctctaatcgatgcaagccctctcttttcctta Intra-Species Hit: Count: 1 Min: 1 Max: 153 Len: 153 Subject: tfor_TF1448_TF1449|possible competence protein:RNA polymerase sigma factor, RpoD|POSITIVE:POSITIVE|[1533111,1533263]|153 HSP 1 e-value: 3.0E-69 bit: 262.0 Len: 153 Query Start:1 Query End:153 Subject Strand: POSITIVE Subject Start: 1 Subject End: 153 tgacaatgctctatctgacgattgttttgttttatgattcatatcgtcgtcttatcctctcnnnnnnngaaatcccggaaatgcactgcacgtccgagactttttcagaagaaagtaattgctctaatcgatgcaagccctctcttttcctta tgacaatgctctatctgacgattgttttgttttatgattcatatcgtcgtcttatcctctcaaaaaaagaaatcccggaaatgcactgcacgtccgagactttttcagaagaaagtaattgctctaatcgatgcaagccctctcttttcctta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGACAAUGCUCUAUCUGACGAUUGUUUUGUUUUAUGAUUCAUAUCGUCGUCUUAUCCUCUCAAAAAAAGAAAUCCCGGAAAUGCACUGCACGUCCGAGACUUUUUCAGAAGAAAGUAAUUGCUCUAAUCGAUGCAAGCCCUCUCUUUUCCUUA ................((((((((..(..(...)..)..)).))))))..................(((((.((.((((..(((...)))..)))).)).))))).((((((.((...((((((.....)).))))...)).))))))..... (-27.10) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAGGAAAAGAGAGGGCUUGCAUCGAUUAGAGCAAUUACUUUCUUCUGAAAAAGUCUCGGACGUGCAGUGCAUUUCCGGGAUUUCUUUUUUUGAGAGGAUAAGACGACGAUAUGAAUCAUAAAACAAAACAAUCGUCAGAUAGAGCAUUGUCA .........((.((.((((..(((..............(((((((((.(((((((((((((.((((...)))).)))))))).....))))).)))))).)))..((((((.((...............)))))))).))).)))).)).)). (-40.66) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 351 140 91 80 34 tfor:TF1975|5end_uridylate_kinase_2121536..2121766_POSITIVE 305 111 73 167 118 tfor:TF1745|5end_hypothetical_protein_1879154..1879384_POSITIVE 301 90 44 141 98 tfor:TF0435|5end_DNA_mismatch_repair_protein_457182..457412_POSITIVE 300 144 106 118 77 tfor:TF2966|5end_hypothetical_protein_3176948..3177178_POSITIVE 296 139 91 117 56 tfor:TF1624|5end_carboxyl-terminal_protease_1737252..1737482_POSITIVE 292 89 42 93 37 tfor:TF2766|5end_shikimate_kinase_2951619..2951849_POSITIVE 292 96 71 72 41 tfor:TF0001|5end_hypothetical_protein_-116..114_POSITIVE 287 100 65 98 67 tfor:TF2018|5end_hypothetical_protein_2175077..2175307_POSITIVE 282 64 23 180 129 tfor:TF1296|5end_possible_DNA-binding_protein,_histone-like_family_1378432..1378662_POSITIVE 281 96 60 197 153 tfor:TF1555|5end_hypothetical_protein_1661061..1661291_POSITIVE 277 150 129 227 209 tfor:TF3149|5end_conserved_hypothetical_protein_3384424..3384654_POSITIVE 275 113 76 204 162 tfor:TF0606|5end_signal_peptidase_II_636816..637046_POSITIVE 273 130 81 174 104 tfor:TF0941|5end_transposase_fragment_981973..982203_POSITIVE 273 140 93 51 6 tfor:TF0114|5end_conserved_hypothetical_protein_123852..124082_POSITIVE 272 106 74 68 30 tfor:TF1912|5end_transcriptional_regulator,_TetR_family_2065970..2066200_POSITIVE 272 96 57 224 191 tfor:TF0809|5end_cation_efflux_protein_865358..865588_POSITIVE 269 140 91 175 123 tfor:TF1730|5end_diaminopimelate_decarboxylase_1854670..1854900_POSITIVE 269 140 91 124 72 tfor:TF1732|5end_conserved_hypothetical_protein_1854619..1854849_POSITIVE 269 50 1 107 49 tfor:TF1585|5end_hypothetical_protein_1690369..1690599_POSITIVE 269 50 1 107 49 tfor:TF1584|5end_hypothetical_protein_1690245..1690475_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 305 111 73 151 102 tfor:TF1744|3end_phenylacetate-CoA_ligase_1879218..1879368_POSITIVE 300 144 106 52 11 tfor:TF2965|3end_conserved_hypothetical_protein_3176962..3177112_POSITIVE 296 139 91 117 56 tfor:TF1623|3end_5-formyltetrahydrofolate_cyclo-ligase_1737332..1737482_POSITIVE 287 100 65 42 11 tfor:TF2017|3end_conserved_hypothetical_protein_2175101..2175251_POSITIVE 281 96 60 69 25 tfor:TF1554|3end_UDP-glucose_dehydrogenase_1661013..1661163_POSITIVE 275 85 44 131 88 tfor:TF0268|3end_hypothetical_protein_297032..297182_POSITIVE 269 140 91 143 91 tfor:TF1729|3end_aspartokinase_1854718..1854868_POSITIVE 269 50 1 129 71 tfor:TF1583|3end_conserved_hypothetical_protein;_possible_endonuclease_1690223..1690373_POSITIVE 263 149 121 23 2 tfor:TF0020|3end_possible_glycoprotein_endopeptidase_16029..16179_POSITIVE 257 96 56 100 53 tfor:TF1940|3end_TPR-repeat-containing_protein_2088814..2088964_POSITIVE 257 80 42 118 66 tfor:TF0673|3end_conserved_hypothetical_protein_717355..717505_POSITIVE 255 60 19 136 96 tfor:TF2770|3end_conserved_hypothetical_protein_2956639..2956789_POSITIVE 254 98 55 120 74 tfor:TF0061|3end_hypothetical_protein_65006..65156_POSITIVE 248 106 74 57 23 tfor:TF3010|3end_possible_anti-sigma_factor_3230888..3231038_POSITIVE 247 88 41 121 69 tfor:TF2617|3end_conserved_hypothetical_protein_2795172..2795322_POSITIVE 247 90 44 112 64 tfor:TF2549|3end_30S_ribosomal_protein_S7_2732345..2732495_POSITIVE 245 57 15 93 49 tfor:TF2896|3end_conserved_hypothetical_protein;_possible_ATPase,_AAA_superfamily_3085687..3085837_POSITIVE 243 114 76 85 43 tfor:TF1619|3end_riboflavin_synthase,_beta_subunit_1734528..1734678_POSITIVE 243 89 43 148 103 tfor:TF1397|3end_glucosyltransferase_1471534..1471684_POSITIVE 243 118 74 54 3 tfor:TF0433|3end_60_kDa_inner_membrane_protein_455386..455536_POSITIVE