Origin IGS: ttaacttattgtactgaccccaaaaagttgaacaaatttaatttaacttactaataaggattgacttctgtaagaagcaggagttaatccttttagttttattttttcaataatatctatatcttttttatcttcacatgttagtctacctcatgaaaaaactgccctaaaatcttggacacaagattagaggtgcagtacaaaattctttcttataaaaataagttgaaaatcttattgttttgtgttacaatgttcaaacaaagaggtgatgaat .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9 attcatcacctctttgtttgaacattgtaacacaaaacaataagattttcaacttatttttataagaaagaattttgtactgcacctctaatcttgtgtccaagattttagggcagttttttcatgaggtagactaacatgtgaagataaaaaagatatagatattattgaaaaaataaaactaaaaggattaactcctgcttcttacagaagtcaatccttattagtaagttaaattaaatttgttcaactttttggggtcagtacaataagttaa Mask Tandem Repeat Region ================================================ ttaacttattgtactgaccccaaaaagttgaacaaatttaatttaacttactaataaggattgacttctgtaagaagcaggagttaatccttttagttttattttttcaataatatctatatcttttttatcttcacatgttagtctacctcatgaaaaaactgccctaaaatcttggacacaagattagaggtgcagtacaaaattctttcttataaaaataagttgaaaatcttattgttttgtgttacaatgttcaaacaaagaggtgatgaat Find is-nt database================================================ Query_seq: FN0209:FN0210|FN0209:FN0210:Hypothetical cytosolic protein:Transcriptional regulator, COPG family:->->:836861..837137 277 ttaacttattgtactgaccccaaaaagttgaacaaatttaatttaacttactaataaggattgacttctgtaagaagcaggagttaatccttttagttttattttttcaataatatctatatcttttttatcttcacatgttagtctacctcatgaaaaaactgccctaaaatcttggacacaagattagaggtgcagtacaaaattctttcttataaaaataagttgaaaatcttattgttttgtgttacaatgttcaaacaaagaggtgatgaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN0209:FN0210|FN0209:FN0210:Hypothetical cytosolic protein:Transcriptional regulator, COPG family:->->:836861..837137 277 ttaacttattgtactgaccccaaaaagttgaacaaatttaatttaacttactaataaggattgacttctgtaagaagcaggagttaatccttttagttttattttttcaataatatctatatcttttttatcttcacatgttagtctacctcatgaaaaaactgccctaaaatcttggacacaagattagaggtgcagtacaaaattctttcttataaaaataagttgaaaatcttattgttttgtgttacaatgttcaaacaaagaggtgatgaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN0209:FN0210|FN0209:FN0210:Hypothetical cytosolic protein:Transcriptional regulator, COPG family:->->:836861..837137 277 ttaacttattgtactgaccccaaaaagttgaacaaatttaatttaacttactaataaggattgacttctgtaagaagcaggagttaatccttttagttttattttttcaataatatctatatcttttttatcttcacatgttagtctacctcatgaaaaaactgccctaaaatcttggacacaagattagaggtgcagtacaaaattctttcttataaaaataagttgaaaatcttattgttttgtgttacaatgttcaaacaaagaggtgatgaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttaacttattgtactgaccccaaaaagttgaacaaatttaatttaacttactaataaggattgacttctgtaagaagcaggagttaatccttttagttttattttttcaataatatctatatcttttttatcttcacatgttagtctacctcatgaaaaaactgccctaaaatcttggacacaagattagaggtgcagtacaaaattctttcttataaaaataagttgaaaatcttattgttttgtgttacaatgttcaaacaaagaggtgatgaat Predict ORF larger than 30AA ================================================ Protein_Len: 35 Strand: + Start: 172 End: 276 ........................................................................................................................................................................... M L D T R L E V Q Y K I L S Y K N K L K I L L F C V T M F K Q R G D E . ttaacttattgtactgaccccaaaaagttgaacaaatttaatttaacttactaataaggattgacttctgtaagaagcaggagttaatccttttagttttattttttcaataatatctatatcttttttatcttcacatgttagtctacctcatgaaaaaactgccctaaaatcttggacacaagattagaggtgcagtacaaaattctttcttataaaaataagttgaaaatcttattgttttgtgttacaatgttcaaacaaagaggtgatgaat Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ PromScan Matrix: RpoD-17 Strand: + Score: 89 Start: 225 End: 254 ................................................................................................................................................................................................................................GTTGAAAATCTTATTGTTTTGTGTTACAAT....................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ ttaacttattgtactgaccccaaaaagttgaacaaatttaatttaacttactaataaggattgacttctgtaagaagcaggagttaatccttttagttttattttttcaataatatctatatcttttttatcttcacatgttagtctacctcatgaaaaaactgccctaaaatcttggacacaagattagaggtgcagtacaaaattctttcttataaaaataagttgaaaatcttattgttttgtgttacaatgttcaaacaaagaggtgatgaat Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 100 HP_score: -10.8 Tail_Score: -5.43553 Start: 51 End: 96 Full_Region: ATTTAATTTAACTTA CTAATAAGGATTGACTTCTGT AAGAA GCAGGAGTTAATCCTTTTAG TTTTATTTTTTCAAT ..................................................CTAATAAGGATTGACTTCTGTAAGAAGCAGGAGTTAATCCTTTTAG..................................................................................................................................................................................... TransTerm Strand: - Conf: 55 HP_score: -5.7 Tail_Score: -2.57192 Start: 51 End: 96 Full_Region: attgaaaaaataaaa ctaaaaggattaactcctg cttctta cagaagtcaatccttattag taagttaaattaaat ..................................................ctaaaaggattaactcctgcttcttacagaagtcaatccttattag..................................................................................................................................................................................... TransTerm Strand: - Conf: 58 HP_score: -4.9 Tail_Score: -3.75105 Start: 58 End: 90 Full_Region: aaaataaaactaaaa ggattaactcctg cttctta cagaagtcaatcc ttattagtaagttaa .........................................................ggattaactcctgcttcttacagaagtcaatcc........................................................................................................................................................................................... TransTerm Strand: - Conf: 93 HP_score: -7.4 Tail_Score: -5.15634 Start: 162 End: 198 Full_Region: agaaagaattttgta ctgcacctctaatcttg tgtc caagattttagggcag ttttttcatgaggta .................................................................................................................................................................ctgcacctctaatcttgtgtccaagattttagggcag............................................................................... Find igs database================================================ Query_seq: FN0209:FN0210|FN0209:FN0210:Hypothetical cytosolic protein:Transcriptional regulator, COPG family:->->:836861..837137 277 ttaacttattgtactgaccccaaaaagttgaacaaatttaatttaacttactaataaggattgacttctgtaagaagcaggagttaatccttttagttttattttttcaataatatctatatcttttttatcttcacatgttagtctacctcatgaaaaaactgccctaaaatcttggacacaagattagaggtgcagtacaaaattctttcttataaaaataagttgaaaatcttattgttttgtgttacaatgttcaaacaaagaggtgatgaat Intra-Species Hit: Count: 1 Min: 1 Max: 277 Len: 277 Subject: NC_003454_FN0209_FN0210|Hypothetical cytosolic protein:Transcriptional regulator, COPG family|POSITIVE:POSITIVE|[836861,837137]|277 HSP 1 e-value: 3.0E-77 bit: 289.0 Len: 146 Query Start:132 Query End:277 Subject Strand: POSITIVE Subject Start: 132 Subject End: 277 ...................................................................................................................................cttcacatgttagtctacctcatgaaaaaactgccctaaaatcttggacacaagattagaggtgcagtacaaaattctttcttataaaaataagttgaaaatcttattgttttgtgttacaatgttcaaacaaagaggtgatgaat ...................................................................................................................................cttcacatgttagtctacctcatgaaaaaactgccctaaaatcttggacacaagattagaggtgcagtacaaaattctttcttataaaaataagttgaaaatcttattgttttgtgttacaatgttcaaacaaagaggtgatgaat HSP 2 e-value: 7.0E-44 bit: 178.0 Len: 90 Query Start:1 Query End:90 Subject Strand: POSITIVE Subject Start: 1 Subject End: 90 ttaacttattgtactgaccccaaaaagttgaacaaatttaatttaacttactaataaggattgacttctgtaagaagcaggagttaatcc........................................................................................................................................................................................... ttaacttattgtactgaccccaaaaagttgaacaaatttaatttaacttactaataaggattgacttctgtaagaagcaggagttaatcc........................................................................................................................................................................................... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUAACUUAUUGUACUGACCCCAAAAAGUUGAACAAAUUUAAUUUAACUUACUAAUAAGGAUUGACUUCUGUAAGAAGCAGGAGUUAAUCCUUUUAGUUUUAUUUUUUCAAUAAUAUCUAUAUCUUUUUUAUCUUCACAUGUUAGUCUACCUCAUGAAAAAACUGCCCUAAAAUCUUGGACACAAGAUUAGAGGUGCAGUACAAAAUUCUUUCUUAUAAAAAUAAGUUGAAAAUCUUAUUGUUUUGUGUUACAAUGUUCAAACAAAGAGGUGAUGAAU ............((((((......((((((((.........))))))))(((((.((((((((((((((((.....)))))))))))))))))))))..........................................)))))).((((((........((((((((..(((((((....)))))))..))).)))))......(((...(((((....)))))..))).....((((((........))))))..........))))))...... (-66.60) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUUCAUCACCUCUUUGUUUGAACAUUGUAACACAAAACAAUAAGAUUUUCAACUUAUUUUUAUAAGAAAGAAUUUUGUACUGCACCUCUAAUCUUGUGUCCAAGAUUUUAGGGCAGUUUUUUCAUGAGGUAGACUAACAUGUGAAGAUAAAAAAGAUAUAGAUAUUAUUGAAAAAAUAAAACUAAAAGGAUUAACUCCUGCUUCUUACAGAAGUCAAUCCUUAUUAGUAAGUUAAAUUAAAUUUGUUCAACUUUUUGGGGUCAGUACAAUAAGUUAA .......(((((......((((.................((((((((((...(((((....)))))..))))))))))(((((.(((..(((((((....)))))))..))))))))...)))).))))).((((....((((..(((.((((((..((((((.(((((.....))))).((((((((((((.(((.(((.......))).))).))))))).)))))............))))))....))))))...)))..))))...)))).. (-59.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 603 199 153 71 28 NC_003454:FN0839|5end_hypothetical_protein_1501426..1501656_NEGATIVE 553 199 160 201 161 NC_003454:FN1444|5end_GMP_synthase_[glutamine-hydrolyzing]_2111585..2111815_POSITIVE 495 60 11 131 79 NC_003454:FN1530|5end_Transposase_43625..43855_POSITIVE 493 199 151 137 88 NC_003454:FN1443|5end_Transposase_2111518..2111748_NEGATIVE 493 199 151 137 88 NC_003454:FN0786|5end_Transposase_1442465..1442695_POSITIVE 493 199 151 137 88 NC_003454:FN0135|5end_Transposase_770238..770468_POSITIVE 429 209 161 145 96 NC_003454:FN0485|5end_Transposase_1130267..1130497_POSITIVE 387 199 151 135 88 NC_003454:FN0840|5end_Transposase_1501361..1501591_POSITIVE 378 199 156 222 178 NC_003454:FN1972|5end_hypothetical_protein_472071..472301_NEGATIVE 366 198 151 123 76 NC_003454:FN1446|5end_Transposase_2116033..2116263_POSITIVE 366 198 151 135 88 NC_003454:FN1887|5end_Transposase_371671..371901_POSITIVE 340 97 56 210 168 NC_003454:FN0864|5end_hypothetical_protein_1522900..1523130_NEGATIVE 316 100 56 208 166 NC_003454:FN0496|5end_hypothetical_protein_1140910..1141140_POSITIVE 277 94 56 159 121 NC_003454:FN1997|5end_Transcriptional_regulator_499758..499988_POSITIVE 262 100 68 225 189 NC_003454:FN0846|5end_hypothetical_protein_1504242..1504472_POSITIVE 250 111 76 104 65 NC_003454:FN0807|5end_3-deoxy-manno-octulosonate_cytidylyltransferase_1467894..1468124_NEGATIVE 246 98 58 166 127 NC_003454:FN1343|5end_seC-independent_protein_TATD_1997232..1997462_NEGATIVE 238 104 69 160 124 NC_003454:FN1753|5end_thiamine_biosynthesis_protein_ThiH_250344..250574_NEGATIVE 236 135 91 177 139 NC_003454:FN0654|5end_phosphoglycerate_kinase_1312107..1312337_POSITIVE 229 150 101 152 96 NC_003454:FN0724|5end_flavodoxin_1384167..1384397_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 785 90 41 138 89 NC_003454:FN1447|3end_Transposase_2117342..2117492_POSITIVE 785 90 41 138 89 NC_003454:FN0841|3end_Transposase_1502804..1502954_POSITIVE 785 90 41 138 89 NC_003454:FN0486|3end_Transposase_1131710..1131860_POSITIVE 785 90 41 138 89 NC_003454:FN0139|3end_Transposase_771640..771790_POSITIVE 785 90 41 138 89 NC_003454:FN1889|3end_Transposase_373027..373177_POSITIVE 711 90 41 138 89 NC_003454:FN1442|3end_Transposase_2110155..2110305_NEGATIVE 711 90 41 138 89 NC_003454:FN0787|3end_Transposase_1443908..1444058_POSITIVE 662 90 41 138 89 NC_003454:FN1680|3end_Transposase_175971..176121_NEGATIVE 645 202 161 46 4 NC_003454:FN1019|3end_3-hydroxybutyryl-CoA_dehydrogenase_1672945..1673095_NEGATIVE 613 210 161 98 49 NC_003454:FN1904|3end_Transcriptional_regulator,_MarR_family_393633..393783_POSITIVE 548 199 160 81 41 NC_003454:FN1463|3end_pyridoxine_biosynthesis_protein_2145924..2146074_POSITIVE 533 199 160 79 39 NC_003454:FN1499|3end_Cell_surface_protein_5166..5316_POSITIVE 501 98 65 34 1 NC_003454:FN1800|3end_Peptidyl-prolyl_cis-trans_isomerase_282534..282684_POSITIVE 464 210 161 85 36 NC_003454:FN1547|3end_PTS_permease_for_N-acetylglucosamine_and_glucose_61801..61951_NEGATIVE 436 199 157 76 33 NC_003454:FN1546|3end_translation_elongation_factor_EF-G_59529..59679_NEGATIVE 429 209 161 70 21 NC_003454:FN0484|3end_Lipase_1130272..1130422_POSITIVE 429 200 153 85 45 NC_003454:FN0436|3end_Urea_carboxylase_1077851..1078001_NEGATIVE 404 199 154 77 30 NC_003454:FN1498|3end_Integral_membrane_protein_3542..3692_POSITIVE 395 107 72 35 1 NC_003454:FN1530|3end_Transposase_44061..44211_POSITIVE 389 199 152 67 23 NC_003454:FN0177|3end_Cell_division_inhibitor_MinE_802336..802486_POSITIVE