Origin IGS: tggatacacaagtgaaacaaagtgtgtgataaaagaaagtctcaccaataaattgagatatttcaaatcctccatcattacactattacaatgtgatgatggaaagaatagaatgaaatacatttcaagtgcgaaatcatatttctgctatacatcataaatgaacatcctcttatagaggctatcgttcaaaaacaagcaaatgacaatttgaaataacaaaagataaattaggggagtatacttgaaaagtttactccccttttgtgttataaaaat .........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 atttttataacacaaaaggggagtaaacttttcaagtatactcccctaatttatcttttgttatttcaaattgtcatttgcttgtttttgaacgatagcctctataagaggatgttcatttatgatgtatagcagaaatatgatttcgcacttgaaatgtatttcattctattctttccatcatcacattgtaatagtgtaatgatggaggatttgaaatatctcaatttattggtgagactttcttttatcacacactttgtttcacttgtgtatcca Mask Tandem Repeat Region ================================================ tggatacacaagtgaaacaaagtgtgtgataaaagaaagtctcaccaataaattgagatatttcaaatcctccatcattacactattacaatgtgatgatggaaagaatagaatgaaatacatttcaagtgcgaaatcatatttctgctatacatcataaatgaacatcctcttatagaggctatcgttcaaaaacaagcaaatgacaatttgaaataacaaaagataaattaggggagtatacttgaaaagtttactccccttttgtgttataaaaat Find is-nt database================================================ Query_seq: TDE2453:TDE2454|TDE2453:TDE2454:hypothetical protein:hypothetical protein:-><-:2482162..2482440 279 tggatacacaagtgaaacaaagtgtgtgataaaagaaagtctcaccaataaattgagatatttcaaatcctccatcattacactattacaatgtgatgatggaaagaatagaatgaaatacatttcaagtgcgaaatcatatttctgctatacatcataaatgaacatcctcttatagaggctatcgttcaaaaacaagcaaatgacaatttgaaataacaaaagataaattaggggagtatacttgaaaagtttactccccttttgtgttataaaaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE2453:TDE2454|TDE2453:TDE2454:hypothetical protein:hypothetical protein:-><-:2482162..2482440 279 tggatacacaagtgaaacaaagtgtgtgataaaagaaagtctcaccaataaattgagatatttcaaatcctccatcattacactattacaatgtgatgatggaaagaatagaatgaaatacatttcaagtgcgaaatcatatttctgctatacatcataaatgaacatcctcttatagaggctatcgttcaaaaacaagcaaatgacaatttgaaataacaaaagataaattaggggagtatacttgaaaagtttactccccttttgtgttataaaaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE2453:TDE2454|TDE2453:TDE2454:hypothetical protein:hypothetical protein:-><-:2482162..2482440 279 tggatacacaagtgaaacaaagtgtgtgataaaagaaagtctcaccaataaattgagatatttcaaatcctccatcattacactattacaatgtgatgatggaaagaatagaatgaaatacatttcaagtgcgaaatcatatttctgctatacatcataaatgaacatcctcttatagaggctatcgttcaaaaacaagcaaatgacaatttgaaataacaaaagataaattaggggagtatacttgaaaagtttactccccttttgtgttataaaaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tggatacacaagtgaaacaaagtgtgtgataaaagaaagtctcaccaataaattgagatatttcaaatcctccatcattacactattacaatgtgatgatggaaagaatagaatgaaatacatttcaagtgcgaaatcatatttctgctatacatcataaatgaacatcctcttatagaggctatcgttcaaaaacaagcaaatgacaatttgaaataacaaaagataaattaggggagtatacttgaaaagtttactccccttttgtgttataaaaat Predict ORF larger than 30AA ================================================ Protein_Len: 44 Strand: + Start: 26 End: 157 ......................... M I K E S L T N K L R Y F K S S I I T L L Q C D D G K N R M K Y I S S A K S Y F C Y T S .......................................................................................................................... Protein_Len: 33 Strand: + Start: 118 End: 216 ..................................................................................................................... M H F K C E I I F L L Y I I N E H P L I E A I V Q K Q A N D N L K ............................................................... Protein_Len: 43 Strand: - Start: 151 End: 279 ...................................................................................................................................................... V D Y I F M R K Y L S D N L F L C I V I Q F L L L Y I L P T Y K F L K S G K Q T I F M Protein_Len: 35 Strand: - Start: 81 End: 185 ................................................................................ V I V I H H H F S Y F S I C K L H S I M N R S Y M M F S C G R I S A M .............................................................................................. Protein_Len: 41 Strand: - Start: 1 End: 123 P Y V L S V F H T I F S L R V L L N L Y K L D E M M V S N C H S S P F F L I F Y M ............................................................................................................................................................ tggatacacaagtgaaacaaagtgtgtgataaaagaaagtctcaccaataaattgagatatttcaaatcctccatcattacactattacaatgtgatgatggaaagaatagaatgaaatacatttcaagtgcgaaatcatatttctgctatacatcataaatgaacatcctcttatagaggctatcgttcaaaaacaagcaaatgacaatttgaaataacaaaagataaattaggggagtatacttgaaaagtttactccccttttgtgttataaaaat 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================================================ tggatacacaagtgaaacaaagtgtgtgataaaagaaagtctcaccaataaattgagatatttcaaatcctccatcattacactattacaatgtgatgatggaaagaatagaatgaaatacatttcaagtgcgaaatcatatttctgctatacatcataaatgaacatcctcttatagaggctatcgttcaaaaacaagcaaatgacaatttgaaataacaaaagataaattaggggagtatacttgaaaagtttactccccttttgtgttataaaaat Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 100 HP_score: -14.7 Tail_Score: -4.73682 Start: 234 End: 262 Full_Region: ACAAAAGATAAATTA GGGGAGTATACTT GAA AAGTTTACTCCCC TTTTGTGTTATAAAA .........................................................................................................................................................................................................................................GGGGAGTATACTTGAAAAGTTTACTCCCC................. Find igs database================================================ Query_seq: TDE2453:TDE2454|TDE2453:TDE2454:hypothetical protein:hypothetical protein:-><-:2482162..2482440 279 tggatacacaagtgaaacaaagtgtgtgataaaagaaagtctcaccaataaattgagatatttcaaatcctccatcattacactattacaatgtgatgatggaaagaatagaatgaaatacatttcaagtgcgaaatcatatttctgctatacatcataaatgaacatcctcttatagaggctatcgttcaaaaacaagcaaatgacaatttgaaataacaaaagataaattaggggagtatacttgaaaagtttactccccttttgtgttataaaaat Intra-Species Hit: Count: 1 Min: 1 Max: 279 Len: 279 Subject: NC_002967_TDE2453_TDE2454|hypothetical protein:hypothetical protein|POSITIVE:NEGATIVE|[2482162,2482440]|279 HSP 1 e-value: 1.0E-156 bit: 553.0 Len: 279 Query Start:1 Query End:279 Subject Strand: POSITIVE Subject Start: 1 Subject End: 279 tggatacacaagtgaaacaaagtgtgtgataaaagaaagtctcaccaataaattgagatatttcaaatcctccatcattacactattacaatgtgatgatggaaagaatagaatgaaatacatttcaagtgcgaaatcatatttctgctatacatcataaatgaacatcctcttatagaggctatcgttcaaaaacaagcaaatgacaatttgaaataacaaaagataaattaggggagtatacttgaaaagtttactccccttttgtgttataaaaat tggatacacaagtgaaacaaagtgtgtgataaaagaaagtctcaccaataaattgagatatttcaaatcctccatcattacactattacaatgtgatgatggaaagaatagaatgaaatacatttcaagtgcgaaatcatatttctgctatacatcataaatgaacatcctcttatagaggctatcgttcaaaaacaagcaaatgacaatttgaaataacaaaagataaattaggggagtatacttgaaaagtttactccccttttgtgttataaaaat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGGAUACACAAGUGAAACAAAGUGUGUGAUAAAAGAAAGUCUCACCAAUAAAUUGAGAUAUUUCAAAUCCUCCAUCAUUACACUAUUACAAUGUGAUGAUGGAAAGAAUAGAAUGAAAUACAUUUCAAGUGCGAAAUCAUAUUUCUGCUAUACAUCAUAAAUGAACAUCCUCUUAUAGAGGCUAUCGUUCAAAAACAAGCAAAUGACAAUUUGAAAUAACAAAAGAUAAAUUAGGGGAGUAUACUUGAAAAGUUUACUCCCCUUUUGUGUUAUAAAAAU .(((((((((..(......)..))))).......((((((((((.........)))))).))))..))))((((((((((((.........))))))))))))..(.((((...((((((.(((((......)))))..))))))..)))).)........(((((..((((.....)))).....)))))........(((((....)))))..((((((...((......(((((((((.(((.....))).))))))))).)).))))))...... (-68.60) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUUUUUAUAACACAAAAGGGGAGUAAACUUUUCAAGUAUACUCCCCUAAUUUAUCUUUUGUUAUUUCAAAUUGUCAUUUGCUUGUUUUUGAACGAUAGCCUCUAUAAGAGGAUGUUCAUUUAUGAUGUAUAGCAGAAAUAUGAUUUCGCACUUGAAAUGUAUUUCAUUCUAUUCUUUCCAUCAUCACAUUGUAAUAGUGUAAUGAUGGAGGAUUUGAAAUAUCUCAAUUUAUUGGUGAGACUUUCUUUUAUCACACACUUUGUUUCACUUGUGUAUCCA .........(((((..(((((((((.(((.....))).)))))))))..........(((.(((((((((((......((((..(...((((((....((((.....)))).))))))...)..).))).....(((((((.((((((....)))))))))))))...........((((((((.((((((...)))))).)))))))).)))))))))))...)))......((((((((....................)))))))))))))..... (-74.35) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 262 201 168 135 96 NC_002967:TDE0073|5end_riboflavin_biosynthesis_protein_RibF,_putative_84082..84312_NEGATIVE 257 263 225 184 130 NC_002967:TDE2097|5end_hypothetical_protein_2124741..2124971_NEGATIVE 245 268 233 146 117 NC_002967:TDE1910|5end_1-deoxy-D-xylulose-5-phosphate_synthase_1928837..1929067_NEGATIVE 230 263 225 74 25 NC_002967:TDE1057|5end_hypothetical_protein_1086245..1086475_NEGATIVE 224 239 192 78 33 NC_002967:TDE2516|5end_hypothetical_protein_2542021..2542251_POSITIVE 220 269 238 99 69 NC_002967:TDE2149|5end_transglycosylase,_SLT_family_2187293..2187523_NEGATIVE 219 189 145 124 74 NC_002967:TDE2767|5end_flagellar_protein-related_protein_2821093..2821323_NEGATIVE 217 188 147 116 82 NC_002967:TDE1948|5end_ABC_transporter,_permease_protein_1964551..1964781_NEGATIVE 216 263 231 193 145 NC_002967:TDE2024|5end_hypothetical_protein_2051021..2051251_NEGATIVE 214 208 168 133 95 NC_002967:TDE1771|5end_hypothetical_protein_1815358..1815588_NEGATIVE 211 170 123 213 172 NC_002967:TDE0118|5end_hypothetical_protein_137047..137277_NEGATIVE 211 187 147 190 136 NC_002967:TDE0004|5end_hypothetical_protein_4243..4473_POSITIVE 208 108 61 151 96 NC_002967:TDE2625|5end_ABC_transporter,_ATP-binding/permease_protein_2666664..2666894_NEGATIVE 208 155 113 192 155 NC_002967:TDE2295|5end_mechanosensitive_ion_channel_family_protein_2333334..2333564_POSITIVE 204 210 162 47 2 NC_002967:TDE2300|5end_trypsin_domain/PDZ_domain_protein_2341434..2341664_NEGATIVE 203 184 141 200 158 NC_002967:TDE1236|5end_triosephosphate_isomerase_1269486..1269716_POSITIVE 203 184 141 90 48 NC_002967:TDE1235|5end_hypothetical_protein_1269376..1269606_POSITIVE 203 190 158 102 73 NC_002967:TDE1043|5end_hypothetical_protein_1070945..1071175_POSITIVE 203 180 131 123 68 NC_002967:TDE0778|5end_ribosomal_protein_L24_811487..811717_POSITIVE 202 55 11 56 4 NC_002967:TDE2706|5end_hypothetical_protein_2753793..2754023_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 262 201 168 61 22 NC_002967:TDE0074|3end_amino_acid_permease_family_protein_84156..84306_NEGATIVE 245 268 233 40 11 NC_002967:TDE1911|3end_hypothetical_protein_1928943..1929093_NEGATIVE 242 183 145 90 56 NC_002967:TDE1133|3end_hypothetical_protein_1164753..1164903_NEGATIVE 230 263 225 87 38 NC_002967:TDE1058|3end_hypothetical_protein_1086232..1086382_NEGATIVE 225 270 225 82 28 NC_002967:TDE2178|3end_hypothetical_protein_2206683..2206833_NEGATIVE 222 270 229 80 29 NC_002967:TDE2170|3end_hypothetical_protein_2201606..2201756_NEGATIVE 222 262 226 39 3 NC_002967:TDE0978|3end_hypothetical_protein_1002424..1002574_POSITIVE 220 269 238 138 108 NC_002967:TDE2150|3end_hypothetical_protein_2187254..2187404_NEGATIVE 220 270 234 43 8 NC_002967:TDE0723|3end_hypothetical_protein_761661..761811_POSITIVE 219 189 145 98 48 NC_002967:TDE2768|3end_flagellar_hook_protein_2821119..2821269_NEGATIVE 217 188 147 123 89 NC_002967:TDE1949|3end_ABC_transporter,_ATP-binding_protein_1964544..1964694_NEGATIVE 216 263 231 139 91 NC_002967:TDE2025|3end_hypothetical_protein_2051075..2051225_NEGATIVE 216 265 233 85 42 NC_002967:TDE0665|3end_pyruvate_ferredoxin/flavodoxin_oxidoreductase_family_protein_699792..699942_NEGATIVE 214 208 168 48 10 NC_002967:TDE1772|3end_hypothetical_protein_1815443..1815593_NEGATIVE 212 76 38 129 88 NC_002967:TDE2441|3end_hypothetical_protein_2472356..2472506_NEGATIVE 211 187 147 149 95 NC_002967:TDE0003|3end_hypothetical_protein_4282..4432_POSITIVE 210 264 231 85 38 NC_002967:TDE2420|3end_DNA-directed_RNA_polymerase_beta'_subunit_2444960..2445110_NEGATIVE 208 270 221 75 20 NC_002967:TDE1650|3end_ABC_transporter,_ATP-binding_protein_1697377..1697527_NEGATIVE 207 190 142 39 1 NC_002967:TDE1225|3end_zinc_ABC_transporter,_ATP-binding_protein_1258751..1258901_NEGATIVE 206 48 3 58 14 NC_002967:TDE2313|3end_hypothetical_protein_2349506..2349656_NEGATIVE