Origin IGS: taaaatttgccttgcccgaaatgggtatagtgcgatcagctgacaataaaaacctctcctcccgcccacagcggcgggaggagagatataaacaataaccaaatgtttcacgattaaaaaatcagaatt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aattctgattttttaatcgtgaaacatttggttattgtttatatctctcctcccgccgctgtgggcgggaggagaggtttttattgtcagctgatcgcactatacccatttcgggcaaggcaaatttta Mask Tandem Repeat Region ================================================ taaaatttgccttgcccgaaatgggtatagtgcgatcagctgacaataaaaacctctcctcccgcccacagcggcgggaggagagatataaacaataaccaaatgtttcacgattaaaaaatcagaatt Find is-nt database================================================ Query_seq: TF0027:TF0028|TF0027:TF0028:conserved hypothetical protein:hypothetical protein:->->:24260..24388 129 taaaatttgccttgcccgaaatgggtatagtgcgatcagctgacaataaaaacctctcctcccgcccacagcggcgggaggagagatataaacaataaccaaatgtttcacgattaaaaaatcagaatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF0027:TF0028|TF0027:TF0028:conserved hypothetical protein:hypothetical protein:->->:24260..24388 129 taaaatttgccttgcccgaaatgggtatagtgcgatcagctgacaataaaaacctctcctcccgcccacagcggcgggaggagagatataaacaataaccaaatgtttcacgattaaaaaatcagaatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF0027:TF0028|TF0027:TF0028:conserved hypothetical protein:hypothetical protein:->->:24260..24388 129 taaaatttgccttgcccgaaatgggtatagtgcgatcagctgacaataaaaacctctcctcccgcccacagcggcgggaggagagatataaacaataaccaaatgtttcacgattaaaaaatcagaatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taaaatttgccttgcccgaaatgggtatagtgcgatcagctgacaataaaaacctctcctcccgcccacagcggcgggaggagagatataaacaataaccaaatgtttcacgattaaaaaatcagaatt Predict ORF larger than 30AA ================================================ Protein_Len: 38 Strand: - Start: 1 End: 114 L I Q R A R F P Y L A I L Q C Y F G R R G G V A A P P S I Y V I V L H K V M ............... taaaatttgccttgcccgaaatgggtatagtgcgatcagctgacaataaaaacctctcctcccgcccacagcggcgggaggagagatataaacaataaccaaatgtttcacgattaaaaaatcagaatt 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================================================ taaaatttgccttgcccgaaatgggtatagtgcgatcagctgacaataaaaacctctcctcccgcccacagcggcgggaggagagatataaacaataaccaaatgtttcacgattaaaaaatcagaatt Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 100 HP_score: -20.4 Tail_Score: -5.19328 Start: 53 End: 86 Full_Region: tggttattgtttata tctctcctcccgcc gctgtg ggcgggaggagagg tttttattgtcagct ....................................................tctctcctcccgccgctgtgggcgggaggagagg........................................... TransTerm Strand: - Conf: 100 HP_score: -21.7 Tail_Score: -3.70512 Start: 54 End: 85 Full_Region: ggttattgtttatat ctctcctcccgcc gctgtg ggcgggaggagag gtttttattgtcagc .....................................................ctctcctcccgccgctgtgggcgggaggagag............................................ Find igs database================================================ Query_seq: TF0027:TF0028|TF0027:TF0028:conserved hypothetical protein:hypothetical protein:->->:24260..24388 129 taaaatttgccttgcccgaaatgggtatagtgcgatcagctgacaataaaaacctctcctcccgcccacagcggcgggaggagagatataaacaataaccaaatgtttcacgattaaaaaatcagaatt Intra-Species Hit: Count: 1 Min: 1 Max: 129 Len: 129 Subject: tfor_TF0027_TF0028|conserved hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[24260,24388]|129 HSP 1 e-value: 2.0E-67 bit: 256.0 Len: 129 Query Start:1 Query End:129 Subject Strand: POSITIVE Subject Start: 1 Subject End: 129 taaaatttgccttgcccgaaatgggtatagtgcgatcagctgacaataaaaacctctcctcccgcccacagcggcgggaggagagatataaacaataaccaaatgtttcacgattaaaaaatcagaatt taaaatttgccttgcccgaaatgggtatagtgcgatcagctgacaataaaaacctctcctcccgcccacagcggcgggaggagagatataaacaataaccaaatgtttcacgattaaaaaatcagaatt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAAAUUUGCCUUGCCCGAAAUGGGUAUAGUGCGAUCAGCUGACAAUAAAAACCUCUCCUCCCGCCCACAGCGGCGGGAGGAGAGAUAUAAACAAUAACCAAAUGUUUCACGAUUAAAAAAUCAGAAUU ......(((((((((((.....))))).)).))))....((((..........(((((((((((((......)))))))))))))....(((((.........))))).............)))).... (-43.50) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUUCUGAUUUUUUAAUCGUGAAACAUUUGGUUAUUGUUUAUAUCUCUCCUCCCGCCGCUGUGGGCGGGAGGAGAGGUUUUUAUUGUCAGCUGAUCGCACUAUACCCAUUUCGGGCAAGGCAAAUUUUA ..((((((((....))))).)))....(..(((((.((....(((((((((((((((......)))))))))))))))....)).)).)))..)..((.((...(((.....)))..))))........ (-44.50) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 382 89 52 177 137 tfor:TF1586|5end_hypothetical_protein_1690971..1691201_POSITIVE 359 79 31 164 111 tfor:TF2375|5end_conserved_hypothetical_protein_2540953..2541183_POSITIVE 358 80 33 138 75 tfor:TF2039|5end_possible_cell-cycle_regulation_histidine_triad_(HIT)_protein_2199318..2199548_POSITIVE 356 80 31 185 122 tfor:TF3110|5end_conserved_hypothetical_protein_with_helicase_domain_3342714..3342944_POSITIVE 354 43 6 230 193 tfor:TF2934|5end_acetyltransferase/carbonic_anhydrase_3136647..3136877_POSITIVE 343 87 53 45 11 tfor:TF2746|5end_hypothetical_protein_2927996..2928226_POSITIVE 342 78 32 190 132 tfor:TF0449|5end_transposase_467891..468121_POSITIVE 336 82 53 172 130 tfor:TF2504|5end_peptidyl-prolyl_cis-trans_isomerase_2680031..2680261_POSITIVE 334 87 51 52 19 tfor:TF2895|5end_hypothetical_protein_3083936..3084166_POSITIVE 328 87 59 95 63 tfor:TF0528|5end_two-component_system_sensor_histidine_kinase_552357..552587_POSITIVE 327 85 41 222 178 tfor:TF0001|5end_hypothetical_protein_-116..114_POSITIVE 325 59 11 213 152 tfor:TF2758|5end_hypothetical_protein_2942392..2942622_POSITIVE 323 99 53 54 13 tfor:TF0021|5end_outer_membrane_phospholipase_A_15949..16179_POSITIVE 320 79 32 87 33 tfor:TF2439|5end_conserved_hypothetical_protein_2616380..2616610_POSITIVE 320 79 35 89 41 tfor:TF1548|5end_thiophene_and_furan_oxidation_protein_1652501..1652731_POSITIVE 319 78 33 168 124 tfor:TF1343|5end_hypothetical_protein_1424630..1424860_POSITIVE 318 85 54 155 126 tfor:TF2712|5end_glycosyltransferase_2885918..2886148_POSITIVE 317 85 53 32 1 tfor:TF2640|5end_hypothetical_protein_2809106..2809336_POSITIVE 317 79 33 208 148 tfor:TF0145|5end_glutamine_synthetase_152446..152676_POSITIVE 316 84 51 109 71 tfor:TF3135|5end_hypothetical_protein_3369821..3370051_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 566 85 54 37 6 tfor:TF0027|3end_conserved_hypothetical_protein_24199..24349_POSITIVE 342 78 32 130 72 tfor:TF0448|3end_hypothetical_protein_467911..468061_POSITIVE 335 67 21 114 66 tfor:TF0001|3end_hypothetical_protein_158..308_POSITIVE 334 79 34 130 86 tfor:TF0350|3end_hypothetical_protein_371101..371251_POSITIVE 327 85 41 58 14 tfor:TF3165|3end_thiol:disulfide_interchange_protein,_thioredoxin_family_protein_3405343..3405493_POSITIVE 325 59 11 76 15 tfor:TF2757|3end_hypothetical_protein_2942335..2942485_POSITIVE 323 99 53 54 13 tfor:TF0020|3end_possible_glycoprotein_endopeptidase_16029..16179_POSITIVE 322 87 41 137 92 tfor:TF0643|3end_probable_tRNA_methyltransferase_685690..685840_POSITIVE 319 78 33 78 34 tfor:TF1342|3end_possible_lipoprotein_1424620..1424770_POSITIVE 316 84 51 121 83 tfor:TF3133|3end_conserved_hypothetical_protein_3369913..3370063_POSITIVE 315 81 52 132 85 tfor:TF2607|3end_conserved_hypothetical_protein_2784645..2784795_POSITIVE 315 83 52 52 20 tfor:TF1438|3end_hypothetical_protein_1522524..1522674_POSITIVE 312 80 53 71 38 tfor:TF3153|3end_conserved_hypothetical_protein_3389324..3389474_POSITIVE 310 81 53 136 95 tfor:TF2188|3end_conserved_hypothetical_protein_2363535..2363685_POSITIVE 309 94 53 73 21 tfor:TF0516|3end_conserved_hypothetical_protein;_possible_membrane_protein_540693..540843_POSITIVE 308 85 54 127 83 tfor:TF2893|3end_conserved_hypothetical_protein;_possible_phosphoesterase_3082039..3082189_POSITIVE 308 77 38 134 82 tfor:TF2342|3end_glutathione_peroxidase_2506639..2506789_POSITIVE 305 75 31 45 8 tfor:TF2449|3end_undecaprenyl_diphosphate_synthase_2626541..2626691_POSITIVE 303 94 53 134 93 tfor:TF2924|3end_DNA-binding_response_regulator/sensor_histidine_kinase_3125618..3125768_POSITIVE 302 87 53 117 63 tfor:TF0351|3end_hypothetical_protein_371226..371376_POSITIVE