Origin IGS: tgaaggtagaagcaacgactccggatacagcctgttttgcatctgcctaaggagatatcatcgtgttaatgtagattaaatttgttatctatcgtgtatat .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 atatacacgatagataacaaatttaatctacattaacacgatgatatctccttaggcagatgcaaaacaggctgtatccggagtcgttgcttctaccttca Mask Tandem Repeat Region ================================================ tgaaggtagaagcaacgactccggatacagcctgttttgcatctgcctaaggagatatcatcgtgttaatgtagattaaatttgttatctatcgtgtatat Find is-nt database================================================ Query_seq: TF0652:TF0653|TF0652:TF0653:conserved hypothetical protein:hypothetical protein:->->:696583..696683 101 tgaaggtagaagcaacgactccggatacagcctgttttgcatctgcctaaggagatatcatcgtgttaatgtagattaaatttgttatctatcgtgtatat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF0652:TF0653|TF0652:TF0653:conserved hypothetical protein:hypothetical protein:->->:696583..696683 101 tgaaggtagaagcaacgactccggatacagcctgttttgcatctgcctaaggagatatcatcgtgttaatgtagattaaatttgttatctatcgtgtatat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF0652:TF0653|TF0652:TF0653:conserved hypothetical protein:hypothetical protein:->->:696583..696683 101 tgaaggtagaagcaacgactccggatacagcctgttttgcatctgcctaaggagatatcatcgtgttaatgtagattaaatttgttatctatcgtgtatat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tgaaggtagaagcaacgactccggatacagcctgttttgcatctgcctaaggagatatcatcgtgttaatgtagattaaatttgttatctatcgtgtatat Predict ORF larger than 30AA ================================================ tgaaggtagaagcaacgactccggatacagcctgttttgcatctgcctaaggagatatcatcgtgttaatgtagattaaatttgttatctatcgtgtatat 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================================================ tgaaggtagaagcaacgactccggatacagcctgttttgcatctgcctaaggagatatcatcgtgttaatgtagattaaatttgttatctatcgtgtatat Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TF0652:TF0653|TF0652:TF0653:conserved hypothetical protein:hypothetical protein:->->:696583..696683 101 tgaaggtagaagcaacgactccggatacagcctgttttgcatctgcctaaggagatatcatcgtgttaatgtagattaaatttgttatctatcgtgtatat Intra-Species Hit: Count: 1 Min: 1 Max: 101 Len: 101 Subject: tfor_TF0652_TF0653|conserved hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[696583,696683]|101 HSP 1 e-value: 6.0E-51 bit: 200.0 Len: 101 Query Start:1 Query End:101 Subject Strand: POSITIVE Subject Start: 1 Subject End: 101 tgaaggtagaagcaacgactccggatacagcctgttttgcatctgcctaaggagatatcatcgtgttaatgtagattaaatttgttatctatcgtgtatat tgaaggtagaagcaacgactccggatacagcctgttttgcatctgcctaaggagatatcatcgtgttaatgtagattaaatttgttatctatcgtgtatat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGAAGGUAGAAGCAACGACUCCGGAUACAGCCUGUUUUGCAUCUGCCUAAGGAGAUAUCAUCGUGUUAAUGUAGAUUAAAUUUGUUAUCUAUCGUGUAUAU ...(((((((.((((.(((...((......)).))))))).)))))))..(((((((.((.....(((((....)))))...)).))))).))........ (-22.00) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUAUACACGAUAGAUAACAAAUUUAAUCUACAUUAACACGAUGAUAUCUCCUUAGGCAGAUGCAAAACAGGCUGUAUCCGGAGUCGUUGCUUCUACCUUCA ........(.(((((..........)))))).......((((((...((((....((((.((.....))..))))....))))))))))............ (-15.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 409 48 4 208 157 tfor:TF0358|5end_hypothetical_protein_375616..375846_POSITIVE 369 48 9 119 80 tfor:TF1476|5end_outer_membrane_protein_P49_1569723..1569953_POSITIVE 354 57 13 227 178 tfor:TF1249|5end_phosphoglycerate_kinase_(cytosolic_phosphoglycerate_kinase)_1331017..1331247_POSITIVE 335 54 12 49 3 tfor:TF3065|5end_enolase_3291055..3291285_POSITIVE 332 45 3 176 130 tfor:TF0759|5end_heat_shock_protein_15,_RNA-binding_domain_S4_805870..806100_POSITIVE 331 52 18 62 28 tfor:TF2704|5end_ribonuclease_HII_2876242..2876472_POSITIVE 327 70 23 61 1 tfor:TF2248|5end_transfer_region-related_protein,_TraB_2422551..2422781_POSITIVE 317 54 11 83 34 tfor:TF2108|5end_hypothetical_protein_2277385..2277615_POSITIVE 316 46 4 186 141 tfor:TF1845|5end_hypothetical_protein_1996620..1996850_POSITIVE 316 46 4 186 141 tfor:TF1185|5end_hypothetical_protein_1269238..1269468_POSITIVE 307 47 5 113 58 tfor:TF1436|5end_phosphoglycolate_phosphatase_1521128..1521358_POSITIVE 304 49 2 180 137 tfor:TF2655|5end_DNA_topoisomerase_I_2824543..2824773_POSITIVE 304 55 15 72 23 tfor:TF0797|5end_conserved_hypothetical_protein_853296..853526_POSITIVE 304 50 4 78 34 tfor:TF0202|5end_folylpolyglutamate_synthase_227717..227947_POSITIVE 300 48 5 179 128 tfor:TF1489|5end_argininosuccinate_lyase_1588904..1589134_POSITIVE 299 65 21 92 46 tfor:TF1531|5end_potassium_uptake_protein_1636534..1636764_POSITIVE 298 55 15 117 66 tfor:TF0080|5end_phosphate_ABC_transporter,_periplasmic_phosphate-binding_protein_86325..86555_POSITIVE 294 99 65 136 102 tfor:TF1882|5end_conserved_hypothetical_protein_2033987..2034217_POSITIVE 294 48 1 101 45 tfor:TF1585|5end_hypothetical_protein_1690369..1690599_POSITIVE 294 48 1 101 45 tfor:TF1584|5end_hypothetical_protein_1690245..1690475_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 354 57 13 58 9 tfor:TF1247|3end_alanyl-tRNA_synthetase_(alanine--tRNA_ligase)_1330928..1331078_POSITIVE 331 52 18 57 23 tfor:TF2703|3end_conserved_hypothetical_protein_2876317..2876467_POSITIVE 317 54 11 54 5 tfor:TF2107|3end_hypothetical_protein_2277436..2277586_POSITIVE 316 46 4 135 90 tfor:TF2745|3end_hypothetical_protein_2927947..2928097_POSITIVE 313 48 1 61 7 tfor:TF0624|3end_Xaa-Pro_dipeptidase_(aminopeptidase_P)_661015..661165_POSITIVE 307 68 21 97 49 tfor:TF0604|3end_hypothetical_protein_636196..636346_POSITIVE 304 49 2 116 73 tfor:TF2654|3end_arginyl-tRNA_synthetase_2824559..2824709_POSITIVE 304 50 4 54 10 tfor:TF0201|3end_permease,_major_facilitator_superfamily_227773..227923_POSITIVE 299 65 21 92 46 tfor:TF1530|3end_1-deoxyxylulose-5-phosphate_synthase_1636614..1636764_POSITIVE 294 99 65 121 87 tfor:TF1881|3end_hypothetical_protein_2034052..2034202_POSITIVE 294 48 1 123 67 tfor:TF1583|3end_conserved_hypothetical_protein;_possible_endonuclease_1690223..1690373_POSITIVE 293 47 5 141 93 tfor:TF1293|3end_ATPase,_possible_AAA_superfamily_1375924..1376074_POSITIVE 290 43 5 79 41 tfor:TF3104|3end_outer_membrane_protein,_TonB_dependent_receptor_3337450..3337600_POSITIVE 289 65 21 92 40 tfor:TF0464|3end_precorrin_methylase_482108..482258_POSITIVE 287 71 31 56 5 tfor:TF2247|3end_transfer_region-related_protein,_TraA_2422625..2422775_POSITIVE 287 48 1 80 14 tfor:TF1050|3end_hypothetical_protein_1111951..1112101_POSITIVE 286 70 21 51 5 tfor:TF2906|3end_phosphatidylserine_decarboxylase_3102933..3103083_POSITIVE 284 48 10 77 40 tfor:TF0795|3end_hypothetical_protein_853199..853349_POSITIVE 281 46 4 96 51 tfor:TF1186|3end_hypothetical_protein_1269815..1269965_POSITIVE 277 65 27 108 62 tfor:TF3006|3end_response_regulator,_transcriptional_regulator_RprY_3227162..3227312_POSITIVE