Origin IGS: tgattatggatatcgataccccggatgatatggcaaagttccaattccttaaagaatattttacctattgagcattacacaaatcgtacatgttaataaagaatcattgctgtcgtacatttgcactattactgattttaacgtgagttcgatctaagcggtcatcaatcttgagttatccataatctcctgatagaggtttatggagggtttcttctcaaagaaagaaa .........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 tttctttctttgagaagaaaccctccataaacctctatcaggagattatggataactcaagattgatgaccgcttagatcgaactcacgttaaaatcagtaatagtgcaaatgtacgacagcaatgattctttattaacatgtacgatttgtgtaatgctcaataggtaaaatattctttaaggaattggaactttgccatatcatccggggtatcgatatccataatca Mask Tandem Repeat Region ================================================ tgattatggatatcgataccccggatgatatggcaaagttccaattccttaaagaatattttacctattgagcattacacaaatcgtacatgttaataaagaatcattgctgtcgtacatttgcactattactgattttaacgtgagttcgatctaagcggtcatcaatcttgagttatccataatctcctgatagaggtttatggagggtttcttctcaaagaaagaaa Find is-nt database================================================ Query_seq: TF1875:TF1876|TF1875:TF1876:conserved hypothetical protein:hypothetical protein:->->:2029654..2029883 230 tgattatggatatcgataccccggatgatatggcaaagttccaattccttaaagaatattttacctattgagcattacacaaatcgtacatgttaataaagaatcattgctgtcgtacatttgcactattactgattttaacgtgagttcgatctaagcggtcatcaatcttgagttatccataatctcctgatagaggtttatggagggtttcttctcaaagaaagaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF1875:TF1876|TF1875:TF1876:conserved hypothetical protein:hypothetical protein:->->:2029654..2029883 230 tgattatggatatcgataccccggatgatatggcaaagttccaattccttaaagaatattttacctattgagcattacacaaatcgtacatgttaataaagaatcattgctgtcgtacatttgcactattactgattttaacgtgagttcgatctaagcggtcatcaatcttgagttatccataatctcctgatagaggtttatggagggtttcttctcaaagaaagaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF1875:TF1876|TF1875:TF1876:conserved hypothetical protein:hypothetical protein:->->:2029654..2029883 230 tgattatggatatcgataccccggatgatatggcaaagttccaattccttaaagaatattttacctattgagcattacacaaatcgtacatgttaataaagaatcattgctgtcgtacatttgcactattactgattttaacgtgagttcgatctaagcggtcatcaatcttgagttatccataatctcctgatagaggtttatggagggtttcttctcaaagaaagaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tgattatggatatcgataccccggatgatatggcaaagttccaattccttaaagaatattttacctattgagcattacacaaatcgtacatgttaataaagaatcattgctgtcgtacatttgcactattactgattttaacgtgagttcgatctaagcggtcatcaatcttgagttatccataatctcctgatagaggtttatggagggtttcttctcaaagaaagaaa Predict ORF larger than 30AA ================================================ Protein_Len: 33 Strand: + Start: 56 End: 154 ....................................................... M F Y L L S I T Q I V H V N K E S L L S Y I C T I T D F N V S S I ............................................................................ Protein_Len: 30 Strand: - Start: 64 End: 153 ............................................................... R N L M V C I T C T L L S D N S D Y M Q V I V S K L T L E M ............................................................................. tgattatggatatcgataccccggatgatatggcaaagttccaattccttaaagaatattttacctattgagcattacacaaatcgtacatgttaataaagaatcattgctgtcgtacatttgcactattactgattttaacgtgagttcgatctaagcggtcatcaatcttgagttatccataatctcctgatagaggtttatggagggtttcttctcaaagaaagaaa Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ PromScan Matrix: RpoD-17 Strand: - Score: 81 Start: 25 End: 54 ........................CTTTAAGGAATTGGAACTTTGCCATATCAT................................................................................................................................................................................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tgattatggatatcgataccccggatgatatggcaaagttccaattccttaaagaatattttacctattgagcattacacaaatcgtacatgttaataaagaatcattgctgtcgtacatttgcactattactgattttaacgtgagttcgatctaagcggtcatcaatcttgagttatccataatctcctgatagaggtttatggagggtttcttctcaaagaaagaaa Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TF1875:TF1876|TF1875:TF1876:conserved hypothetical protein:hypothetical protein:->->:2029654..2029883 230 tgattatggatatcgataccccggatgatatggcaaagttccaattccttaaagaatattttacctattgagcattacacaaatcgtacatgttaataaagaatcattgctgtcgtacatttgcactattactgattttaacgtgagttcgatctaagcggtcatcaatcttgagttatccataatctcctgatagaggtttatggagggtttcttctcaaagaaagaaa Intra-Species Hit: Count: 1 Min: 1 Max: 230 Len: 230 Subject: tfor_TF1875_TF1876|conserved hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[2029654,2029883]|230 HSP 1 e-value: 1.0E-127 bit: 456.0 Len: 230 Query Start:1 Query End:230 Subject Strand: POSITIVE Subject Start: 1 Subject End: 230 tgattatggatatcgataccccggatgatatggcaaagttccaattccttaaagaatattttacctattgagcattacacaaatcgtacatgttaataaagaatcattgctgtcgtacatttgcactattactgattttaacgtgagttcgatctaagcggtcatcaatcttgagttatccataatctcctgatagaggtttatggagggtttcttctcaaagaaagaaa tgattatggatatcgataccccggatgatatggcaaagttccaattccttaaagaatattttacctattgagcattacacaaatcgtacatgttaataaagaatcattgctgtcgtacatttgcactattactgattttaacgtgagttcgatctaagcggtcatcaatcttgagttatccataatctcctgatagaggtttatggagggtttcttctcaaagaaagaaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGAUUAUGGAUAUCGAUACCCCGGAUGAUAUGGCAAAGUUCCAAUUCCUUAAAGAAUAUUUUACCUAUUGAGCAUUACACAAAUCGUACAUGUUAAUAAAGAAUCAUUGCUGUCGUACAUUUGCACUAUUACUGAUUUUAACGUGAGUUCGAUCUAAGCGGUCAUCAAUCUUGAGUUAUCCAUAAUCUCCUGAUAGAGGUUUAUGGAGGGUUUCUUCUCAAAGAAAGAAA .(((((((((((.(.........((((((...((.........((((......)))).........(((((((..(((.......)))((((((((...(((((...(((............)))..))).))....)))))))).)))))))....)).))))))........).))))))))))).(((.....)))......(((((....)))))........... (-41.93) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUCUUUCUUUGAGAAGAAACCCUCCAUAAACCUCUAUCAGGAGAUUAUGGAUAACUCAAGAUUGAUGACCGCUUAGAUCGAACUCACGUUAAAAUCAGUAAUAGUGCAAAUGUACGACAGCAAUGAUUCUUUAUUAACAUGUACGAUUUGUGUAAUGCUCAAUAGGUAAAAUAUUCUUUAAGGAAUUGGAACUUUGCCAUAUCAUCCGGGGUAUCGAUAUCCAUAAUCA (((((((......)))))))...........(((.....))).(((((((((((((((..(((.((((...((.(((((((.((....((((((((((......((((....))))........))))).....)))))..)).))))))).))...........((((((..(((((....)))))......)))))).)))))))..)))).....))))))))))). (-48.94) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 339 160 111 123 70 tfor:TF3003|5end_hypothetical_protein_3220382..3220612_POSITIVE 332 200 156 71 32 tfor:TF2322|5end_conserved_hypothetical_protein;_possible_lipoprotein_2482743..2482973_POSITIVE 305 50 2 72 23 tfor:TF0432|5end_3-deoxy-manno-octulosonate_cytidylyltransferase_452531..452761_POSITIVE 303 166 132 82 44 tfor:TF0434|5end_CTP_synthetase_(UTP_ammonia_ligase)_455346..455576_POSITIVE 301 177 131 123 77 tfor:TF1944|5end_conserved_hypothetical_protein_2092516..2092746_POSITIVE 291 177 141 48 7 tfor:TF0244|5end_DNA_recombination_protein_274683..274913_POSITIVE 287 143 102 133 93 tfor:TF2640|5end_hypothetical_protein_2809106..2809336_POSITIVE 287 143 102 47 7 tfor:TF2639|5end_hypothetical_protein_2809020..2809250_POSITIVE 285 227 186 75 36 tfor:TF2468|5end_hypothetical_protein_2646287..2646517_POSITIVE 284 184 142 92 58 tfor:TF2495|5end_succinate-semialdehyde_dehydrogenase_(NADP+)_2669456..2669686_POSITIVE 274 200 153 210 165 tfor:TF1973|5end_propionyl-CoA_carboxylase,_beta_subunit_2119360..2119590_POSITIVE 272 194 157 81 28 tfor:TF1251|5end_riboflavin_synthase,_alpha_subunit_1333744..1333974_POSITIVE 272 41 8 171 137 tfor:TF0947|5end_extracellular_protease_990627..990857_POSITIVE 270 49 9 116 69 tfor:TF1718|5end_conserved_hypothetical_protein_1840462..1840692_POSITIVE 269 220 179 193 138 tfor:TF1334|5end_hypothetical_protein_1415996..1416226_POSITIVE 267 167 126 42 7 tfor:TF1041|5end_dihydroorotate_dehydrogenase,_catalytic_subunit_1102029..1102259_POSITIVE 267 190 142 199 135 tfor:TF0242|5end_conserved_hypothetical_protein_272439..272669_POSITIVE 266 218 179 194 149 tfor:TF1366|5end_signal_peptidase_I_1446075..1446305_POSITIVE 265 210 161 55 3 tfor:TF3097|5end_conserved_hypothetical_protein_3328661..3328891_POSITIVE 263 173 132 179 133 tfor:TF0864|5end_O-succinylbenzoate--CoA_ligase_914570..914800_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 313 161 139 95 73 tfor:TF0264|3end_ISPg3_(IS195)_transposase_293159..293309_POSITIVE 303 166 132 42 4 tfor:TF0433|3end_60_kDa_inner_membrane_protein_455386..455536_POSITIVE 291 177 141 43 2 tfor:TF0243|3end_conserved_hypothetical_protein_274758..274908_POSITIVE 284 184 142 76 42 tfor:TF2494|3end_NAD-dependent_4-hydroxybutyrate_dehydrogenase_2669520..2669670_POSITIVE 272 194 157 58 5 tfor:TF1250|3end_possible_cation_efflux_pump_1333801..1333951_POSITIVE 270 49 9 68 21 tfor:TF1717|3end_DNA_mismatch_repair_protein_1840494..1840644_POSITIVE 269 220 179 131 76 tfor:TF1333|3end_probable_acylaminoacyl_peptidase;_alanyl_dipeptidyl_peptidase_1416014..1416164_POSITIVE 268 160 111 58 5 tfor:TF0467|3end_acetyltransferase-related_protein_486543..486693_POSITIVE 267 167 126 51 16 tfor:TF1040|3end_dihydroorotate_dehydrogenase,_electron_transfer_subunit_1102118..1102268_POSITIVE 258 38 13 133 107 tfor:TF2654|3end_arginyl-tRNA_synthetase_2824559..2824709_POSITIVE 255 202 161 51 12 tfor:TF1015|3end_conserved_hypothetical_protein_1074115..1074265_POSITIVE 252 42 2 63 19 tfor:TF1734|3end_conserved_hypothetical_protein_1860118..1860268_POSITIVE 251 49 6 149 101 tfor:TF2020|3end_muconate_cycloisomerase_2177552..2177702_POSITIVE 250 159 113 123 69 tfor:TF2805|3end_zinc_protease_2996665..2996815_POSITIVE 249 160 114 123 73 tfor:TF1466|3end_DNA_gyrase_modulator_1557084..1557234_POSITIVE 248 74 38 97 60 tfor:TF2456|3end_ABC_transporter,_ATP-binding_protein_2633208..2633358_POSITIVE 247 49 13 41 11 tfor:TF2575|3end_methionine_aminopeptidase_2745985..2746135_POSITIVE 247 48 4 123 79 tfor:TF2238|3end_conserved_hypothetical_protein_2414588..2414738_POSITIVE 246 207 162 133 88 tfor:TF1186|3end_hypothetical_protein_1269815..1269965_POSITIVE 246 189 152 122 90 tfor:TF1126|3end_conserved_hypothetical_protein;_possible_lipoprotein_1201026..1201176_POSITIVE