Origin IGS: cgtattttgtttttaaaatttgttttgcaaacatatggcatctttttggtgtatccaaatatttttttgtttttattctttttttaactatttgggtttattgttttgtcatctaagcgattttgtttttcttttgaaattgtttctgcaaatgtaaagattttgccgtactcatctgctttttctttctatttagcagggttaacgcatttaaattttcaacaacctcaatcactgaaaattca .........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 tgaattttcagtgattgaggttgttgaaaatttaaatgcgttaaccctgctaaatagaaagaaaaagcagatgagtacggcaaaatctttacatttgcagaaacaatttcaaaagaaaaacaaaatcgcttagatgacaaaacaataaacccaaatagttaaaaaaagaataaaaacaaaaaaatatttggatacaccaaaaagatgccatatgtttgcaaaacaaattttaaaaacaaaatacg Mask Tandem Repeat Region ================================================ cgtattttgtttttaaaatttgttttgcaaacatatggcatctttttggtgtatccaaatatttttttgtttttattctttttttaactatttgggtttattgttttgtcatctaagcgattttgtttttcttttgaaattgtttctgcaaatgtaaagattttgccgtactcatctgctttttctttctatttagcagggttaacgcatttaaattttcaacaacctcaatcactgaaaattca Find is-nt database================================================ Query_seq: TF2027:TF2028|TF2027:TF2028:conserved hypothetical protein:hypothetical protein:->->:2184237..2184481 245 cgtattttgtttttaaaatttgttttgcaaacatatggcatctttttggtgtatccaaatatttttttgtttttattctttttttaactatttgggtttattgttttgtcatctaagcgattttgtttttcttttgaaattgtttctgcaaatgtaaagattttgccgtactcatctgctttttctttctatttagcagggttaacgcatttaaattttcaacaacctcaatcactgaaaattca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF2027:TF2028|TF2027:TF2028:conserved hypothetical protein:hypothetical protein:->->:2184237..2184481 245 cgtattttgtttttaaaatttgttttgcaaacatatggcatctttttggtgtatccaaatatttttttgtttttattctttttttaactatttgggtttattgttttgtcatctaagcgattttgtttttcttttgaaattgtttctgcaaatgtaaagattttgccgtactcatctgctttttctttctatttagcagggttaacgcatttaaattttcaacaacctcaatcactgaaaattca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF2027:TF2028|TF2027:TF2028:conserved hypothetical protein:hypothetical protein:->->:2184237..2184481 245 cgtattttgtttttaaaatttgttttgcaaacatatggcatctttttggtgtatccaaatatttttttgtttttattctttttttaactatttgggtttattgttttgtcatctaagcgattttgtttttcttttgaaattgtttctgcaaatgtaaagattttgccgtactcatctgctttttctttctatttagcagggttaacgcatttaaattttcaacaacctcaatcactgaaaattca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 cgtattttgtttttaaaatttgttttgcaaacatatggcatctttttggtgtatccaaatatttttttgtttttattctttttttaactatttgggtttattgttttgtcatctaagcgattttgtttttcttttgaaattgtttctgcaaatgtaaagattttgccgtactcatctgctttttctttctatttagcagggttaacgcatttaaattttcaacaacctcaatcactgaaaattca Predict ORF larger than 30AA ================================================ Protein_Len: 32 Strand: + Start: 18 End: 113 ................. M C F A N I W H L F G V S K Y F F V F I L F L T I W V Y C F V I .................................................................................................................................... Protein_Len: 45 Strand: + Start: 20 End: 154 ................... M F C K H M A S F W C I Q I F F C F Y S F F N Y L G L L F C H L S D F V F L L K L F L Q M ........................................................................................... Protein_Len: 48 Strand: + Start: 100 End: 243 ................................................................................................... M V L S S K R F C F S F E I V S A N V K I L P Y S S A F S F Y L A G L T H L N F Q Q P Q S L K I .. Protein_Len: 40 Strand: - Start: 116 End: 235 ................................................................................................................... A I K N K K Q F Q K Q L H L S K A T S M Q K K K R N L L T L A N L N E V V E I M .......... Protein_Len: 30 Strand: - Start: 2 End: 91 . Y K T K L I Q K A F M H C R K P T D L Y K K T K I R K K V M .......................................................................................................................................................... cgtattttgtttttaaaatttgttttgcaaacatatggcatctttttggtgtatccaaatatttttttgtttttattctttttttaactatttgggtttattgttttgtcatctaagcgattttgtttttcttttgaaattgtttctgcaaatgtaaagattttgccgtactcatctgctttttctttctatttagcagggttaacgcatttaaattttcaacaacctcaatcactgaaaattca 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================================================ cgtattttgtttttaaaatttgttttgcaaacatatggcatctttttggtgtatccaaatatttttttgtttttattctttttttaactatttgggtttattgttttgtcatctaagcgattttgtttttcttttgaaattgtttctgcaaatgtaaagattttgccgtactcatctgctttttctttctatttagcagggttaacgcatttaaattttcaacaacctcaatcactgaaaattca Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TF2027:TF2028|TF2027:TF2028:conserved hypothetical protein:hypothetical protein:->->:2184237..2184481 245 cgtattttgtttttaaaatttgttttgcaaacatatggcatctttttggtgtatccaaatatttttttgtttttattctttttttaactatttgggtttattgttttgtcatctaagcgattttgtttttcttttgaaattgtttctgcaaatgtaaagattttgccgtactcatctgctttttctttctatttagcagggttaacgcatttaaattttcaacaacctcaatcactgaaaattca Intra-Species Hit: Count: 1 Min: 146 Max: 245 Len: 100 Subject: tfor_TF2027_TF2028|conserved hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[2184237,2184481]|245 HSP 1 e-value: 6.0E-50 bit: 198.0 Len: 100 Query Start:146 Query End:245 Subject Strand: POSITIVE Subject Start: 146 Subject End: 245 .................................................................................................................................................ctgcaaatgtaaagattttgccgtactcatctgctttttctttctatttagcagggttaacgcatttaaattttcaacaacctcaatcactgaaaattca .................................................................................................................................................ctgcaaatgtaaagattttgccgtactcatctgctttttctttctatttagcagggttaacgcatttaaattttcaacaacctcaatcactgaaaattca Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUGCAAAUGUAAAGAUUUUGCCGUACUCAUCUGCUUUUUCUUUCUAUUUAGCAGGGUUAACGCAUUUAAAUUUUCAACAACCUCAAUCACUGAAAAUUCA (((((((((.(((((....((.(.......).))....))))).))))).))))..............((((((((..............)))))))).. (-15.44) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGAAUUUUCAGUGAUUGAGGUUGUUGAAAAUUUAAAUGCGUUAACCCUGCUAAAUAGAAAGAAAAAGCAGAUGAGUACGGCAAAAUCUUUACAUUUGCAG (((((((((((..((....))..)))))))))))............((((.((((..(((((....((...........))....)))))..)))))))) (-20.20) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 352 68 21 170 126 tfor:TF2248|5end_transfer_region-related_protein,_TraB_2422551..2422781_POSITIVE 331 64 21 201 149 tfor:TF2655|5end_DNA_topoisomerase_I_2824543..2824773_POSITIVE 309 66 22 127 80 tfor:TF2566|5end_50S_ribosomal_protein_L5_2740303..2740533_POSITIVE 306 57 23 207 173 tfor:TF1979|5end_conserved_hypothetical_protein_2127957..2128187_POSITIVE 296 65 21 141 89 tfor:TF2513|5end_conserved_hypothetical_protein_2691146..2691376_POSITIVE 279 58 13 56 7 tfor:TF0667|5end_conserved_hypothetical_protein_710982..711212_POSITIVE 278 65 21 224 167 tfor:TF3128|5end_hypothetical_protein_3362253..3362483_POSITIVE 266 45 1 184 138 tfor:TF0463|5end_precorrin-6Y_C5,15-methyltransferase_479015..479245_POSITIVE 259 60 18 82 41 tfor:TF1353|5end_conserved_hypothetical_protein;_possible_penicillinase_repressor_1432908..1433138_POSITIVE 256 55 14 172 116 tfor:TF0693|5end_sigma-54_dependent_transcriptional_regulator_736902..737132_POSITIVE 255 48 1 100 52 tfor:TF1995|5end_exonuclease_2147148..2147378_POSITIVE 254 63 21 209 152 tfor:TF0416|5end_possible_ATP-binding_protein_433134..433364_POSITIVE 253 38 1 68 25 tfor:TF1915|5end_NAD-dependent_protein_deacetylase,_SIR2_family_2067720..2067950_POSITIVE 252 63 22 194 151 tfor:TF0637|5end_TPR-repeat-containing_protein_673195..673425_POSITIVE 251 57 20 108 74 tfor:TF3123|5end_dTDP-4-dehydrorhamnose_3,5-epimerase_3357775..3358005_POSITIVE 245 60 14 103 53 tfor:TF0599|5end_hypothetical_protein_629835..630065_POSITIVE 245 62 22 203 151 tfor:TF0265|5end_conserved_hypothetical_protein,_Rhs_family_293279..293509_POSITIVE 243 85 45 166 126 tfor:TF0449|5end_transposase_467891..468121_POSITIVE 242 52 13 113 57 tfor:TF2043|5end_fructokinase_2202267..2202497_POSITIVE 241 57 30 155 128 tfor:TF1952|5end_immunoreactive_84kD_antigen_PG93_2101443..2101673_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 331 64 21 137 85 tfor:TF2654|3end_arginyl-tRNA_synthetase_2824559..2824709_POSITIVE 309 66 22 127 80 tfor:TF2565|3end_50S_ribosomal_protein_L24_2740383..2740533_POSITIVE 296 65 21 117 65 tfor:TF2512|3end_possible_abortive_infection_protein_2691202..2691352_POSITIVE 278 65 21 125 68 tfor:TF3127|3end_acetyltransferase,_possible_GNAT_family_3362234..3362384_POSITIVE 255 48 1 100 52 tfor:TF1994|3end_acyl-CoA_synthetase_2147228..2147378_POSITIVE 254 63 21 123 66 tfor:TF0414|3end_N-ethylammeline_chlorohydrolase_433128..433278_POSITIVE 251 45 4 61 7 tfor:TF2855|3end_ATPase,_AAA_family_3042011..3042161_POSITIVE 243 85 45 106 66 tfor:TF0448|3end_hypothetical_protein_467911..468061_POSITIVE 242 52 13 122 66 tfor:TF2042|3end_sugar_phosphate_isomerase,_polysialic_acid_capsule_expression_protein_2202356..2202506_POSITIVE 241 57 30 79 52 tfor:TF1951|3end_xanthosine_triphosphate_pyrophosphatase,_Ham1-like_protein_2101447..2101597_POSITIVE 237 57 19 141 104 tfor:TF2358|3end_possible_small-conductance_mechanosensitive_channel_2524850..2525000_POSITIVE 237 45 1 56 19 tfor:TF0075|3end_transcriptional_regulator_83118..83268_POSITIVE 235 44 1 61 14 tfor:TF1063|3end_possible_amidase_enhancer_precursor;_sporulation-related_protein_1134064..1134214_POSITIVE 234 55 20 56 19 tfor:TF0906|3end_conserved_hypothetical_protein_950210..950360_POSITIVE 232 55 20 135 105 tfor:TF2873|3end_conserved_hypothetical_protein_3064966..3065116_POSITIVE 231 65 22 73 20 tfor:TF1341|3end_glycogen_synthase_1423200..1423350_POSITIVE 229 57 26 31 1 tfor:TF1216|3end_possible_ECF-family_RNA_polymerase_sigma_factor_1303902..1304052_POSITIVE 229 33 2 50 22 tfor:TF1206|3end_conserved_hypothetical_protein_1290136..1290286_POSITIVE 228 57 16 151 120 tfor:TF3025|3end_hypothetical_protein_3249091..3249241_POSITIVE 228 62 21 49 11 tfor:TF2184|3end_conserved_hypothetical_protein_2357043..2357193_POSITIVE