Origin IGS: ttatagttttgagtgcattctttatctttgagtataatctccgaaatgcaatcatttgaaaattagcaacttgtattttctcgaaatttttgatgcggttgccctgttgtttattgttta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 taaacaataaacaacagggcaaccgcatcaaaaatttcgagaaaatacaagttgctaattttcaaatgattgcatttcggagattatactcaaagataaagaatgcactcaaaactataa Mask Tandem Repeat Region ================================================ ttatagttttgagtgcattctttatctttgagtataatctccgaaatgcaatcatttgaaaattagcaacttgtattttctcgaaatttttgatgcggttgccctgttgtttattgttta Find is-nt database================================================ Query_seq: TF0891:TF0892|TF0891:TF0892:hypothetical protein:conserved hypothetical protein:->->:940856..940975 120 ttatagttttgagtgcattctttatctttgagtataatctccgaaatgcaatcatttgaaaattagcaacttgtattttctcgaaatttttgatgcggttgccctgttgtttattgttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF0891:TF0892|TF0891:TF0892:hypothetical protein:conserved hypothetical protein:->->:940856..940975 120 ttatagttttgagtgcattctttatctttgagtataatctccgaaatgcaatcatttgaaaattagcaacttgtattttctcgaaatttttgatgcggttgccctgttgtttattgttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF0891:TF0892|TF0891:TF0892:hypothetical protein:conserved hypothetical protein:->->:940856..940975 120 ttatagttttgagtgcattctttatctttgagtataatctccgaaatgcaatcatttgaaaattagcaacttgtattttctcgaaatttttgatgcggttgccctgttgtttattgttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttatagttttgagtgcattctttatctttgagtataatctccgaaatgcaatcatttgaaaattagcaacttgtattttctcgaaatttttgatgcggttgccctgttgtttattgttta Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: - Start: 2 End: 94 . I T K L A N K I K S Y L R R F A I M Q F N A V Q I K E F N K M .......................... ttatagttttgagtgcattctttatctttgagtataatctccgaaatgcaatcatttgaaaattagcaacttgtattttctcgaaatttttgatgcggttgccctgttgtttattgttta 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================================================ ttatagttttgagtgcattctttatctttgagtataatctccgaaatgcaatcatttgaaaattagcaacttgtattttctcgaaatttttgatgcggttgccctgttgtttattgttta Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TF0891:TF0892|TF0891:TF0892:hypothetical protein:conserved hypothetical protein:->->:940856..940975 120 ttatagttttgagtgcattctttatctttgagtataatctccgaaatgcaatcatttgaaaattagcaacttgtattttctcgaaatttttgatgcggttgccctgttgtttattgttta Intra-Species Hit: Count: 1 Min: 1 Max: 120 Len: 120 Subject: tfor_TF0891_TF0892|hypothetical protein:conserved hypothetical protein|POSITIVE:POSITIVE|[940856,940975]|120 HSP 1 e-value: 3.0E-62 bit: 238.0 Len: 120 Query Start:1 Query End:120 Subject Strand: POSITIVE Subject Start: 1 Subject End: 120 ttatagttttgagtgcattctttatctttgagtataatctccgaaatgcaatcatttgaaaattagcaacttgtattttctcgaaatttttgatgcggttgccctgttgtttattgttta ttatagttttgagtgcattctttatctttgagtataatctccgaaatgcaatcatttgaaaattagcaacttgtattttctcgaaatttttgatgcggttgccctgttgtttattgttta Inter-species Hit: Count: 1 Min: 3 Max: 107 Len: 105 Subject: NC_002950_PG0742_PG0744|antigen PgaA:RNA methyltransferase, TrmH family|NEGATIVE:NEGATIVE|[790728,791222]|495 HSP 1 e-value: 2.0E-48 bit: 192.0 Len: 105 Query Start:3 Query End:107 Subject Strand: POSITIVE Subject Start: 113 Subject End: 217 ..atagttttgagtgcattctttatctttgagtataatctccgaaatgcaatcatttgaaaattagcaacttgtattttctcgaaatttttgatgcggttgccctgt............. ..atagttttgagtatattctttatctttgagtataatctccgaaatgcaatcatttgaaaattagcaacttgtattttctcgaaatttttgatgcggttgccctgt............. Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUAGUUUUGAGUGCAUUCUUUAUCUUUGAGUAUAAUCUCCGAAAUGCAAUCAUUUGAAAAUUAGCAACUUGUAUUUUCUCGAAAUUUUUGAUGCGGUUGCCCUGU .......(((.((((((.....((...(((......))).)))))))).)))...........((((((.(((((..............)))))))))))..... (-17.14) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACAGGGCAACCGCAUCAAAAAUUUCGAGAAAAUACAAGUUGCUAAUUUUCAAAUGAUUGCAUUUCGGAGAUUAUACUCAAAGAUAAAGAAUGCACUCAAAACUAU ...((....))................((((((...........))))))...(((.((((((((.(((......)))...)).....)))))).)))....... (-16.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 272 100 51 172 118 tfor:TF0152|5end_RNA_polymerase_ECF-type_sigma_factor_162021..162251_POSITIVE 249 60 19 98 53 tfor:TF1270|5end_hypothetical_protein_1355273..1355503_POSITIVE 246 100 52 152 105 tfor:TF1768|5end_conserved_hypothetical_protein;_possible_transposase_1906526..1906756_POSITIVE 223 100 64 50 10 tfor:TF0210|5end_DNA_polymerase_III,_beta_subunit_235769..235999_POSITIVE 222 48 6 157 122 tfor:TF1586|5end_hypothetical_protein_1690971..1691201_POSITIVE 221 98 56 201 161 tfor:TF2754|5end_hypothetical_protein_2940446..2940676_POSITIVE 217 80 37 52 2 tfor:TF2472|5end_GAF_domain-containing_protein_2649918..2650148_POSITIVE 216 100 55 183 124 tfor:TF2318|5end_conserved_hypothetical_protein_2475603..2475833_POSITIVE 215 44 1 191 143 tfor:TF1077|5end_conserved_hypothetical_protein_1146382..1146612_POSITIVE 215 98 55 121 72 tfor:TF0800|5end_conserved_hypothetical_protein_855864..856094_POSITIVE 214 51 14 230 187 tfor:TF1875|5end_conserved_hypothetical_protein_2028752..2028982_POSITIVE 214 100 69 154 116 tfor:TF1490|5end_hypothetical_protein_1590238..1590468_POSITIVE 214 99 53 79 19 tfor:TF1228|5end_conserved_hypothetical_protein_1314103..1314333_POSITIVE 214 76 34 118 67 tfor:TF0218|5end_translation_initiation_factor_3_(IF-3)_243182..243412_POSITIVE 212 42 2 152 110 tfor:TF2362|5end_conserved_hypothetical_protein_2528321..2528551_POSITIVE 210 51 13 123 78 tfor:TF2556|5end_conserved_hypothetical_protein_2736131..2736361_POSITIVE 210 100 68 35 5 tfor:TF2123|5end_conserved_hypothetical_protein;_TPR-repeat_protein_2297268..2297498_POSITIVE 210 51 14 230 187 tfor:TF1133|5end_conserved_hypothetical_protein_1209618..1209848_POSITIVE 207 68 23 168 123 tfor:TF2293|5end_hypothetical_protein_2447833..2448063_POSITIVE 207 100 57 231 195 tfor:TF0240|5end_conserved_hypothetical_protein;_possible_gycosyltransferase_I_family_protein_270086..270316_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 272 100 51 143 89 tfor:TF0151|3end_hydrolase/beta-alanine_synthase_162072..162222_POSITIVE 228 100 54 125 91 tfor:TF0891|3end_hypothetical_protein_940795..940945_POSITIVE 225 100 60 122 87 tfor:TF0350|3end_hypothetical_protein_371101..371251_POSITIVE 222 43 7 148 112 tfor:TF0196|3end_conserved_hypothetical_protein_221037..221187_POSITIVE 221 98 56 123 83 tfor:TF2753|3end_zinc_protease_2940448..2940598_POSITIVE 214 99 53 127 67 tfor:TF1227|3end_hypothetical_protein_1314231..1314381_POSITIVE 214 100 59 63 28 tfor:TF0939|3end_ISPg1_transposase,_IS1106-related_transposase_981115..981265_POSITIVE 213 100 67 141 112 tfor:TF2879|3end_tRNA_(guanine-N-1)-methyltransferase_3069008..3069158_POSITIVE 211 42 9 124 89 tfor:TF1139|3end_adenylosuccinate_lyase_1216667..1216817_POSITIVE 207 68 23 98 53 tfor:TF2292|3end_hypothetical_protein_2447843..2447993_POSITIVE 207 98 63 150 110 tfor:TF0898|3end_hypothetical_protein_945730..945880_POSITIVE 204 100 63 76 42 tfor:TF2642|3end_acetylornithine_deacetylase_2811827..2811977_POSITIVE 199 98 53 119 70 tfor:TF2255|3end_transfer_region-related_protein,_TraH_2427961..2428111_POSITIVE 199 100 52 119 66 tfor:TF0441|3end_Na+-transporting_NADH:ubiquinone_oxidoreductase,_subunit_3_465314..465464_POSITIVE 197 98 70 26 1 tfor:TF0799|3end_conserved_hypothetical_protein_855849..855999_POSITIVE 197 52 13 146 108 tfor:TF0291|3end_triose-phosphate_isomerase_320131..320281_POSITIVE 196 99 64 80 53 tfor:TF0542|3end_hypothetical_protein_572324..572474_POSITIVE 196 100 63 44 11 tfor:TF0180|3end_carboxynorspermidine_decarboxylase_192480..192630_POSITIVE 194 67 34 53 27 tfor:TF0620|3end_phosphoribosylaminoimidazole-succinocarboxamide_synthase_655735..655885_POSITIVE 193 30 1 128 92 tfor:TF0675|3end_conserved_hypothetical_protein_719019..719169_POSITIVE