Origin IGS: taaatttctccctttaattcataattcttacgacaaagagggtgtactccaacaggcacaccctcttctttcagaacaacaaacaacattattaacagatcgtca .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tgacgatctgttaataatgttgtttgttgttctgaaagaagagggtgtgcctgttggagtacaccctctttgtcgtaagaattatgaattaaagggagaaattta Mask Tandem Repeat Region ================================================ taaatttctccctttaattcataattcttacgacaaagagggtgtactccaacaggcacaccctcttctttcagaacaacaaacaacattattaacagatcgtca Find is-nt database================================================ Query_seq: TF2804:TF2806|TF2804:TF2806:conserved hypothetical protein:conserved hypothetical protein:->->:2994510..2994614 105 taaatttctccctttaattcataattcttacgacaaagagggtgtactccaacaggcacaccctcttctttcagaacaacaaacaacattattaacagatcgtca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF2804:TF2806|TF2804:TF2806:conserved hypothetical protein:conserved hypothetical protein:->->:2994510..2994614 105 taaatttctccctttaattcataattcttacgacaaagagggtgtactccaacaggcacaccctcttctttcagaacaacaaacaacattattaacagatcgtca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF2804:TF2806|TF2804:TF2806:conserved hypothetical protein:conserved hypothetical protein:->->:2994510..2994614 105 taaatttctccctttaattcataattcttacgacaaagagggtgtactccaacaggcacaccctcttctttcagaacaacaaacaacattattaacagatcgtca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taaatttctccctttaattcataattcttacgacaaagagggtgtactccaacaggcacaccctcttctttcagaacaacaaacaacattattaacagatcgtca Predict ORF larger than 30AA ================================================ Protein_Len: 32 Strand: - Start: 3 End: 98 .. I E G K L E Y N K R C L P H V G V P V G E E K L V V F L M I L M ....... taaatttctccctttaattcataattcttacgacaaagagggtgtactccaacaggcacaccctcttctttcagaacaacaaacaacattattaacagatcgtca 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================================================ taaatttctccctttaattcataattcttacgacaaagagggtgtactccaacaggcacaccctcttctttcagaacaacaaacaacattattaacagatcgtca Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 81 HP_score: -9.2 Tail_Score: -3.96892 Start: 38 End: 65 Full_Region: gttgttctgaaagaa gagggtgtgcct gtt ggagtacaccctc tttgtcgtaagaatt .....................................gagggtgtgcctgttggagtacaccctc........................................ Find igs database================================================ Query_seq: TF2804:TF2806|TF2804:TF2806:conserved hypothetical protein:conserved hypothetical protein:->->:2994510..2994614 105 taaatttctccctttaattcataattcttacgacaaagagggtgtactccaacaggcacaccctcttctttcagaacaacaaacaacattattaacagatcgtca Intra-Species Hit: Count: 1 Min: 1 Max: 105 Len: 105 Subject: tfor_TF2804_TF2806|conserved hypothetical protein:conserved hypothetical protein|POSITIVE:POSITIVE|[2994510,2994614]|105 HSP 1 e-value: 3.0E-53 bit: 208.0 Len: 105 Query Start:1 Query End:105 Subject Strand: POSITIVE Subject Start: 1 Subject End: 105 taaatttctccctttaattcataattcttacgacaaagagggtgtactccaacaggcacaccctcttctttcagaacaacaaacaacattattaacagatcgtca taaatttctccctttaattcataattcttacgacaaagagggtgtactccaacaggcacaccctcttctttcagaacaacaaacaacattattaacagatcgtca Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAAUUUCUCCCUUUAAUUCAUAAUUCUUACGACAAAGAGGGUGUACUCCAACAGGCACACCCUCUUCUUUCAGAACAACAAACAACAUUAUUAACAGAUCGUCA ...............................(((..(((((((((.((......)).)))))))))((.....))..........................))). (-18.10) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGACGAUCUGUUAAUAAUGUUGUUUGUUGUUCUGAAAGAAGAGGGUGUGCCUGUUGGAGUACACCCUCUUUGUCGUAAGAAUUAUGAAUUAAAGGGAGAAAUUUA ((((.....))))........(((..(.(((((....((((((((((((((.....).)))))))))))))......))))).)..)))................ (-28.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 514 67 25 203 150 tfor:TF2593|5end_amino_acid_transport_protein_2762882..2763112_POSITIVE 368 70 24 218 158 tfor:TF1505|5end_conserved_hypothetical_protein_1610773..1611003_POSITIVE 354 70 24 163 102 tfor:TF0187|5end_ferredoxin_202151..202381_POSITIVE 353 67 38 228 191 tfor:TF1999|5end_ArgK_protein_with_ATPase_and_kinase_domains_2152769..2152999_POSITIVE 345 68 35 209 177 tfor:TF2664|5end_hypothetical_protein_2841399..2841629_POSITIVE 340 69 24 78 25 tfor:TF1046|5end_hypothetical_protein_1108178..1108408_POSITIVE 337 79 38 214 160 tfor:TF0662|5end_hypothetical_protein_708316..708546_POSITIVE 320 70 37 168 124 tfor:TF0811|5end_conserved_hypothetical_protein;_posible_sugar_phosphate_isomerase_869787..870017_POSITIVE 319 75 32 198 145 tfor:TF3007|5end_conserved_hypothetical_protein_3227256..3227486_POSITIVE 302 71 37 107 74 tfor:TF2795|5end_hypothetical_protein_2980602..2980832_POSITIVE 297 67 35 149 108 tfor:TF2947|5end_isochorismate_synthase_3153633..3153863_POSITIVE 296 67 26 162 112 tfor:TF0476|5end_conserved_hypothetical_protein_494944..495174_POSITIVE 289 67 38 170 132 tfor:TF2536|5end_subtilisin-like_serine_protease_2719286..2719516_POSITIVE 287 66 31 62 30 tfor:TF2676|5end_conserved_hypothetical_protein_2849645..2849875_POSITIVE 285 68 25 159 104 tfor:TF2357|5end_collagenase_2522561..2522791_POSITIVE 283 77 36 161 121 tfor:TF2877|5end_regulatory_protein_3065601..3065831_POSITIVE 277 63 25 190 140 tfor:TF1065|5end_conserved_hypothetical_protein_1135313..1135543_POSITIVE 273 67 30 86 41 tfor:TF0703|5end_conserved_hypothetical_protein_747252..747482_POSITIVE 267 67 28 227 178 tfor:TF0184|5end_dihydroneopterin_aldolase_195629..195859_POSITIVE 266 72 31 231 185 tfor:TF1260|5end_chaperone_protein_DnaJ_1345325..1345555_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 467 71 31 57 4 tfor:TF2592|3end_conserved_hypothetical_protein_2762807..2762957_POSITIVE 353 78 35 64 10 tfor:TF2765|3end_subtilisin-like_serine_protease_2951460..2951610_POSITIVE 353 67 38 65 28 tfor:TF1997|3end_ROK_family_transcriptional_regulator_2152686..2152836_POSITIVE 345 68 35 53 21 tfor:TF2663|3end_hypothetical_protein_2841323..2841473_POSITIVE 340 69 24 65 12 tfor:TF1045|3end_conserved_hypothetical_protein_1108245..1108395_POSITIVE 337 79 38 75 21 tfor:TF0661|3end_hypothetical_protein_708257..708407_POSITIVE 310 67 38 112 74 tfor:TF2413|3end_hypothetical_protein_2590680..2590830_POSITIVE 302 71 37 87 54 tfor:TF2794|3end_possible_transcriptional_regulator_2980662..2980812_POSITIVE 299 75 37 33 2 tfor:TF1169|3end_lipoprotein_ABC_transporter,_permease_component_1251573..1251723_POSITIVE 283 77 36 144 104 tfor:TF2876|3end_cytosine_deaminase_3065664..3065814_POSITIVE 280 67 36 55 24 tfor:TF2804|3end_conserved_hypothetical_protein_2994449..2994599_POSITIVE 261 79 38 80 48 tfor:TF0005|3end_possible_beta-lactamase_1789..1939_POSITIVE 260 71 31 43 2 tfor:TF3077|3end_tonB-dependent_receptor_HmuY_3305766..3305916_POSITIVE 260 74 32 74 19 tfor:TF0105|3end_DNA-binding_stress_protein,_Dps_family_113907..114057_POSITIVE 258 65 29 78 46 tfor:TF2547|3end_hypothetical_protein_2730947..2731097_POSITIVE 256 89 47 65 24 tfor:TF1542|3end_transcriptional_regulator_1649502..1649652_POSITIVE 255 67 35 56 15 tfor:TF1416|3end_outer_membrane_protein_1499413..1499563_POSITIVE 252 67 35 46 5 tfor:TF0182|3end_DNA-binding_protein,_HU-related_195528..195678_POSITIVE 250 80 31 98 39 tfor:TF0287|3end_peptidase,_M23_family_317467..317617_POSITIVE 245 75 41 44 8 tfor:TF2523|3end_NAD(P)H-flavin_oxidoreductase_2702916..2703066_POSITIVE