Origin IGS: tgatgcatataaaacaatgattttgtacaataatctccctgcttcgtacgttaatggttaagaattaaatcacatacgattttaatgcttatctttgtgacagaataacgaataaaaaacagaaaaag .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ctttttctgttttttattcgttattctgtcacaaagataagcattaaaatcgtatgtgatttaattcttaaccattaacgtacgaagcagggagattattgtacaaaatcattgttttatatgcatca Mask Tandem Repeat Region ================================================ tgatgcatataaaacaatgattttgtacaataatctccctgcttcgtacgttaatggttaagaattaaatcacatacgattttaatgcttatctttgtgacagaataacgaataaaaaacagaaaaag Find is-nt database================================================ Query_seq: TF0646:TF0647|TF0646:TF0647:conserved hypothetical protein; possible adenylate cyclase:hypothetical protein:->->:689856..689983 128 tgatgcatataaaacaatgattttgtacaataatctccctgcttcgtacgttaatggttaagaattaaatcacatacgattttaatgcttatctttgtgacagaataacgaataaaaaacagaaaaag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF0646:TF0647|TF0646:TF0647:conserved hypothetical protein; possible adenylate cyclase:hypothetical protein:->->:689856..689983 128 tgatgcatataaaacaatgattttgtacaataatctccctgcttcgtacgttaatggttaagaattaaatcacatacgattttaatgcttatctttgtgacagaataacgaataaaaaacagaaaaag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF0646:TF0647|TF0646:TF0647:conserved hypothetical protein; possible adenylate cyclase:hypothetical protein:->->:689856..689983 128 tgatgcatataaaacaatgattttgtacaataatctccctgcttcgtacgttaatggttaagaattaaatcacatacgattttaatgcttatctttgtgacagaataacgaataaaaaacagaaaaag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tgatgcatataaaacaatgattttgtacaataatctccctgcttcgtacgttaatggttaagaattaaatcacatacgattttaatgcttatctttgtgacagaataacgaataaaaaacagaaaaag Predict ORF larger than 30AA ================================================ tgatgcatataaaacaatgattttgtacaataatctccctgcttcgtacgttaatggttaagaattaaatcacatacgattttaatgcttatctttgtgacagaataacgaataaaaaacagaaaaag 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================================================ tgatgcatataaaacaatgattttgtacaataatctccctgcttcgtacgttaatggttaagaattaaatcacatacgattttaatgcttatctttgtgacagaataacgaataaaaaacagaaaaag Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TF0646:TF0647|TF0646:TF0647:conserved hypothetical protein; possible adenylate cyclase:hypothetical protein:->->:689856..689983 128 tgatgcatataaaacaatgattttgtacaataatctccctgcttcgtacgttaatggttaagaattaaatcacatacgattttaatgcttatctttgtgacagaataacgaataaaaaacagaaaaag Intra-Species Hit: Count: 1 Min: 1 Max: 128 Len: 128 Subject: tfor_TF0646_TF0647|conserved hypothetical protein; possible adenylate cyclase:hypothetical protein|POSITIVE:POSITIVE|[689856,689983]|128 HSP 1 e-value: 6.0E-67 bit: 254.0 Len: 128 Query Start:1 Query End:128 Subject Strand: POSITIVE Subject Start: 1 Subject End: 128 tgatgcatataaaacaatgattttgtacaataatctccctgcttcgtacgttaatggttaagaattaaatcacatacgattttaatgcttatctttgtgacagaataacgaataaaaaacagaaaaag tgatgcatataaaacaatgattttgtacaataatctccctgcttcgtacgttaatggttaagaattaaatcacatacgattttaatgcttatctttgtgacagaataacgaataaaaaacagaaaaag Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGAUGCAUAUAAAACAAUGAUUUUGUACAAUAAUCUCCCUGCUUCGUACGUUAAUGGUUAAGAAUUAAAUCACAUACGAUUUUAAUGCUUAUCUUUGUGACAGAAUAACGAAUAAAAAACAGAAAAAG .((.((((((((((......)))))))............))).))....((((..((.((((.((((((((......)).)))))).)))).))...))))........................... (-13.30) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUUUUUCUGUUUUUUAUUCGUUAUUCUGUCACAAAGAUAAGCAUUAAAAUCGUAUGUGAUUUAAUUCUUAACCAUUAACGUACGAAGCAGGGAGAUUAUUGUACAAAAUCAUUGUUUUAUAUGCAUCA .(((..(((((((.....(((((.(((.......)))((((.((((((.(((....))))))))).)))).....)))))...)))))))..))).(((...((((.....))))...)))....... (-18.70) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 303 78 33 126 81 tfor:TF0864|5end_O-succinylbenzoate--CoA_ligase_914570..914800_POSITIVE 283 78 34 203 163 tfor:TF3136|5end_Na+-translocating_NADH-quinone_reductase,_subunit_F_3369994..3370224_POSITIVE 264 48 18 203 172 tfor:TF0223|5end_conserved_hypothetical_protein_249622..249852_POSITIVE 252 79 36 63 16 tfor:TF1045|5end_conserved_hypothetical_protein_1107665..1107895_POSITIVE 245 47 1 177 129 tfor:TF1684|5end_zinc_protease_1797396..1797626_POSITIVE 245 63 35 91 64 tfor:TF0144|5end_hypothetical_protein_151209..151439_POSITIVE 239 44 1 222 185 tfor:TF2878|5end_conserved_hypothetical_protein;_possible_CAAX_amino_terminal_protease_family_3067304..3067534_POSITIVE 239 51 17 118 79 tfor:TF0065|5end_conserved_hypothetical_protein_70274..70504_POSITIVE 235 63 22 211 165 tfor:TF0327|5end_hypothetical_protein_353718..353948_POSITIVE 231 50 1 132 78 tfor:TF0181|5end_ATP-dependent_DNA_helicase_192408..192638_POSITIVE 230 77 34 99 55 tfor:TF1716|5end_hypothetical_protein_1837442..1837672_POSITIVE 229 58 18 137 92 tfor:TF3100|5end_conserved_hypothetical_protein_3331185..3331415_POSITIVE 227 79 35 172 113 tfor:TF1317|5end_hypothetical_protein_1391378..1391608_POSITIVE 225 112 77 85 45 tfor:TF1326|5end_hypothetical_protein_1403844..1404074_POSITIVE 225 57 15 218 164 tfor:TF1165|5end_conserved_hypothetical_protein_1244873..1245103_POSITIVE 224 58 15 159 109 tfor:TF1889|5end_hypothetical_protein_2041479..2041709_POSITIVE 223 78 36 206 169 tfor:TF2478|5end_hypothetical_protein_2655375..2655605_POSITIVE 223 120 78 172 129 tfor:TF0143|5end_aspartate--ammonia_ligase_151390..151620_POSITIVE 222 74 34 176 143 tfor:TF2824|5end_nucleoside-transporting_protein_nupG_3014701..3014931_POSITIVE 217 58 14 129 68 tfor:TF0659|5end_RNA_polymerase,_ECF-type_sigma_factor_705428..705658_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 283 78 34 42 2 tfor:TF3133|3end_conserved_hypothetical_protein_3369913..3370063_POSITIVE 245 63 35 67 40 tfor:TF0142|3end_subtilisin-like_serine_proteinase_151265..151415_POSITIVE 239 44 1 126 89 tfor:TF2877|3end_regulatory_protein_3067288..3067438_POSITIVE 231 50 1 124 70 tfor:TF0180|3end_carboxynorspermidine_decarboxylase_192480..192630_POSITIVE 225 112 77 107 67 tfor:TF1324|3end_conserved_hypothetical_protein_1403946..1404096_POSITIVE 214 77 36 70 27 tfor:TF2840|3end_hypothetical_protein_3031289..3031439_POSITIVE 213 89 48 95 59 tfor:TF1892|3end_hypothetical_protein_2046340..2046490_POSITIVE 212 63 39 58 29 tfor:TF0040|3end_conserved_hypothetical_protein_43452..43602_POSITIVE 204 57 14 43 2 tfor:TF1164|3end_two-component_system_sensor_histidine_kinase_1244778..1244928_POSITIVE 202 49 9 124 83 tfor:TF2934|3end_acetyltransferase/carbonic_anhydrase_3137245..3137395_POSITIVE 201 66 36 50 20 tfor:TF2239|3end_hypothetical_protein_2414790..2414940_POSITIVE 200 49 2 135 90 tfor:TF2928|3end_predicted_DNA_repair__protein_3131439..3131589_POSITIVE 200 59 16 102 63 tfor:TF2736|3end_methylglyoxal_synthase_2918458..2918608_POSITIVE 199 78 34 51 1 tfor:TF2953|3end_possible_TonB-dependent_outer_membrane_receptor_3161501..3161651_POSITIVE 199 78 44 32 3 tfor:TF2707|3end_glutamine_amidotransferase_2880163..2880313_POSITIVE 199 71 35 103 65 tfor:TF0541|3end_conserved_hypothetical_protein_571858..572008_POSITIVE 197 52 31 142 123 tfor:TF2940|3end_50S_ribosomal_protein_L11_3141890..3142040_POSITIVE 196 71 39 96 60 tfor:TF2694|3end_hypothetical_protein_2870863..2871013_POSITIVE 195 79 36 73 21 tfor:TF0092|3end_outer_membrane_protein_100549..100699_POSITIVE 194 106 85 89 64 tfor:TF0485|3end_transposase_fragment_507624..507774_POSITIVE