Origin IGS: taaatccgagaccttcatttgaagcatcggcgcttgtcttatattgatatgtaccgcttacaaccgacaaggagcgggagggatatcctgatgttcaccgtattttcccgatcttttttcctcccttcaaaattattca .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tgaataattttgaagggaggaaaaaagatcgggaaaatacggtgaacatcaggatatccctcccgctccttgtcggttgtaagcggtacatatcaatataagacaagcgccgatgcttcaaatgaaggtctcggattta Mask Tandem Repeat Region ================================================ taaatccgagaccttcatttgaagcatcggcgcttgtcttatattgatatgtaccgcttacaaccgacaaggagcgggagggatatcctgatgttcaccgtattttcccgatcttttttcctcccttcaaaattattca Find is-nt database================================================ Query_seq: TF2419:TF2420|TF2419:TF2420:conserved hypothetical protein; possible DNA uptake-related protein:hypothetical protein:->->:2599236..2599374 139 taaatccgagaccttcatttgaagcatcggcgcttgtcttatattgatatgtaccgcttacaaccgacaaggagcgggagggatatcctgatgttcaccgtattttcccgatcttttttcctcccttcaaaattattca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF2419:TF2420|TF2419:TF2420:conserved hypothetical protein; possible DNA uptake-related protein:hypothetical protein:->->:2599236..2599374 139 taaatccgagaccttcatttgaagcatcggcgcttgtcttatattgatatgtaccgcttacaaccgacaaggagcgggagggatatcctgatgttcaccgtattttcccgatcttttttcctcccttcaaaattattca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF2419:TF2420|TF2419:TF2420:conserved hypothetical protein; possible DNA uptake-related protein:hypothetical protein:->->:2599236..2599374 139 taaatccgagaccttcatttgaagcatcggcgcttgtcttatattgatatgtaccgcttacaaccgacaaggagcgggagggatatcctgatgttcaccgtattttcccgatcttttttcctcccttcaaaattattca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taaatccgagaccttcatttgaagcatcggcgcttgtcttatattgatatgtaccgcttacaaccgacaaggagcgggagggatatcctgatgttcaccgtattttcccgatcttttttcctcccttcaaaattattca Predict ORF larger than 30AA ================================================ Protein_Len: 45 Strand: + Start: 4 End: 138 ... M R D L H L K H R R L S Y I D M Y R L Q P T R S G R D I L M F T V F S R S F F L P S K L F . taaatccgagaccttcatttgaagcatcggcgcttgtcttatattgatatgtaccgcttacaaccgacaaggagcgggagggatatcctgatgttcaccgtattttcccgatcttttttcctcccttcaaaattattca 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================================================ taaatccgagaccttcatttgaagcatcggcgcttgtcttatattgatatgtaccgcttacaaccgacaaggagcgggagggatatcctgatgttcaccgtattttcccgatcttttttcctcccttcaaaattattca Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TF2419:TF2420|TF2419:TF2420:conserved hypothetical protein; possible DNA uptake-related protein:hypothetical protein:->->:2599236..2599374 139 taaatccgagaccttcatttgaagcatcggcgcttgtcttatattgatatgtaccgcttacaaccgacaaggagcgggagggatatcctgatgttcaccgtattttcccgatcttttttcctcccttcaaaattattca Intra-Species Hit: Count: 1 Min: 1 Max: 139 Len: 139 Subject: tfor_TF2419_TF2420|conserved hypothetical protein; possible DNA uptake-related protein:hypothetical protein|POSITIVE:POSITIVE|[2599236,2599374]|139 HSP 1 e-value: 2.0E-73 bit: 276.0 Len: 139 Query Start:1 Query End:139 Subject Strand: POSITIVE Subject Start: 1 Subject End: 139 taaatccgagaccttcatttgaagcatcggcgcttgtcttatattgatatgtaccgcttacaaccgacaaggagcgggagggatatcctgatgttcaccgtattttcccgatcttttttcctcccttcaaaattattca taaatccgagaccttcatttgaagcatcggcgcttgtcttatattgatatgtaccgcttacaaccgacaaggagcgggagggatatcctgatgttcaccgtattttcccgatcttttttcctcccttcaaaattattca Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAAUCCGAGACCUUCAUUUGAAGCAUCGGCGCUUGUCUUAUAUUGAUAUGUACCGCUUACAACCGACAAGGAGCGGGAGGGAUAUCCUGAUGUUCACCGUAUUUUCCCGAUCUUUUUUCCUCCCUUCAAAAUUAUUCA .................(((((((...(((..(.((((.......)))).)..)))............(((((.(((((((.((((..((.....))..))))))))))).)))))........)))))))........ (-28.60) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGAAUAAUUUUGAAGGGAGGAAAAAAGAUCGGGAAAAUACGGUGAACAUCAGGAUAUCCCUCCCGCUCCUUGUCGGUUGUAAGCGGUACAUAUCAAUAUAAGACAAGCGCCGAUGCUUCAAAUGAAGGUCUCGGAUUUA ..............((((((.......((((........))))...(....)......))))))....((((((.((((..............))))....))))))..((((.(((((....))).)).))))..... (-29.14) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 416 106 62 158 115 tfor:TF3136|5end_Na+-translocating_NADH-quinone_reductase,_subunit_F_3369994..3370224_POSITIVE 369 109 61 174 118 tfor:TF1840|5end_transposase_1990221..1990451_POSITIVE 363 114 78 36 2 tfor:TF1824|5end_ABC_transporter,_ATP-binding_protein_1972537..1972767_POSITIVE 362 110 63 185 133 tfor:TF3108|5end_glutamine-hydrolyzing_carbamoyl-phosphate_synthase,_large_subunit_3338732..3338962_POSITIVE 362 100 51 89 28 tfor:TF1720|5end_conserved_hypothetical_protein_1843679..1843909_POSITIVE 361 100 53 90 45 tfor:TF0642|5end_exported_transglycosylase,_extracellular_solute-binding_protein,_family_3_682796..683026_POSITIVE 359 110 65 120 67 tfor:TF2711|5end_hemolysis_secretion_protein_2884543..2884773_POSITIVE 359 100 53 186 128 tfor:TF2704|5end_ribonuclease_HII_2876242..2876472_POSITIVE 359 100 54 69 27 tfor:TF2038|5end_hypothetical_protein_2198978..2199208_POSITIVE 352 80 31 81 28 tfor:TF0230|5end_hydrolase,_haloacid_dehalogenase-like_family_256982..257212_POSITIVE 351 48 4 49 3 tfor:TF0463|5end_precorrin-6Y_C5,15-methyltransferase_479015..479245_POSITIVE 350 110 63 190 141 tfor:TF2004|5end_thymidylate_synthase_2156372..2156602_POSITIVE 335 110 64 228 175 tfor:TF2597|5end_outer_membrane_receptor_protein;_possible_TonB_dependent_receptor_2767916..2768146_POSITIVE 333 110 65 213 164 tfor:TF1581|5end_hypothetical_protein_1689199..1689429_POSITIVE 332 88 48 136 88 tfor:TF0993|5end_hypothetical_protein_1048457..1048687_POSITIVE 331 110 64 47 3 tfor:TF2398|5end_magnesium_chelatase,_D/I_family_2569549..2569779_POSITIVE 331 90 45 53 1 tfor:TF1668|5end_possible_glycosylhydrolase_1780341..1780571_POSITIVE 331 110 61 68 10 tfor:TF0024|5end_conserved_hypothetical_protein;_possible_ATPase_20191..20421_POSITIVE 330 83 54 63 39 tfor:TF0252|5end_hypothetical_protein_283530..283760_POSITIVE 329 99 54 58 10 tfor:TF2419|5end_conserved_hypothetical_protein;_possible_DNA_uptake-related_protein_2598358..2598588_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 382 102 64 149 112 tfor:TF1815|3end_conserved_hypothetical_protein_1957442..1957592_POSITIVE 362 110 63 109 57 tfor:TF3107|3end_hypothetical_protein_3338736..3338886_POSITIVE 359 110 65 112 59 tfor:TF2710|3end_ABC_transporter,_ATP-binding_protein/permease_component_2884615..2884765_POSITIVE 351 48 4 49 3 tfor:TF0462|3end_possible_cobalamin_biosynthesis_precorrin-3_methylase_479095..479245_POSITIVE 329 99 62 150 115 tfor:TF3135|3end_hypothetical_protein_3370074..3370224_POSITIVE 329 107 64 71 30 tfor:TF1737|3end_outer_membrane_protein,_TonB_dependent_receptor_1865306..1865456_POSITIVE 326 70 21 137 80 tfor:TF2703|3end_conserved_hypothetical_protein_2876317..2876467_POSITIVE 319 80 48 148 116 tfor:TF2530|3end_conserved_hypothetical_protein_2712926..2713076_POSITIVE 315 90 42 138 89 tfor:TF2308|3end_conserved_hypothetical_protein_2468859..2469009_POSITIVE 315 80 32 126 82 tfor:TF1448|3end_possible_competence_protein_1533050..1533200_POSITIVE 315 120 71 82 13 tfor:TF0664|3end_small_protein_B_(SMPB)_709570..709720_POSITIVE 314 84 61 37 6 tfor:TF2404|3end_hypothetical_protein_2579995..2580145_POSITIVE 313 109 64 106 60 tfor:TF2685|3end_iron-regulated_ABC-type_transporter_membrane_component_2862725..2862875_POSITIVE 313 110 61 103 47 tfor:TF2120|3end_holliday_junction_endonuclease_2292760..2292910_POSITIVE 312 117 71 101 51 tfor:TF0350|3end_hypothetical_protein_371101..371251_POSITIVE 310 90 50 119 78 tfor:TF2882|3end_conserved_hypothetical_protein_3074401..3074551_POSITIVE 308 83 44 68 26 tfor:TF3157|3end_sodium/solute_symporter_3393787..3393937_POSITIVE 308 100 54 77 28 tfor:TF2883|3end_peptidyl-prolyl_cis-trans_isomerase_3075129..3075279_POSITIVE 308 110 61 83 17 tfor:TF2264|3end_transfer_region-related_protein,_TraO_2433542..2433692_POSITIVE 308 96 54 96 63 tfor:TF0813|3end_glycosyl_hydrolase,_secreted_872181..872331_POSITIVE