Origin IGS: ttacaaaacataacagattgatcttaaggcataatctgcctttttcgatctctcttcatacgattttcaaaacgatttgtcatctttatctacgctaaattccgtaaatttgcaaaaaaaaagaaagaaagg .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 cctttctttctttttttttgcaaatttacggaatttagcgtagataaagatgacaaatcgttttgaaaatcgtatgaagagagatcgaaaaaggcagattatgccttaagatcaatctgttatgttttgtaa Mask Tandem Repeat Region ================================================ ttacaaaacataacagattgatcttaaggcataatctgcctttttcgatctctcttcatacgattttcaaaacgatttgtcatctttatctacgctaaattccgtaaatttgcaaaaaaaaagaaagaaagg Find is-nt database================================================ Query_seq: TF1529:TF1530|TF1529:TF1530:hypothetical protein:1-deoxyxylulose-5-phosphate synthase:->->:1634617..1634748 132 ttacaaaacataacagattgatcttaaggcataatctgcctttttcgatctctcttcatacgattttcaaaacgatttgtcatctttatctacgctaaattccgtaaatttgcaaaaaaaaagaaagaaagg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF1529:TF1530|TF1529:TF1530:hypothetical protein:1-deoxyxylulose-5-phosphate synthase:->->:1634617..1634748 132 ttacaaaacataacagattgatcttaaggcataatctgcctttttcgatctctcttcatacgattttcaaaacgatttgtcatctttatctacgctaaattccgtaaatttgcaaaaaaaaagaaagaaagg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF1529:TF1530|TF1529:TF1530:hypothetical protein:1-deoxyxylulose-5-phosphate synthase:->->:1634617..1634748 132 ttacaaaacataacagattgatcttaaggcataatctgcctttttcgatctctcttcatacgattttcaaaacgatttgtcatctttatctacgctaaattccgtaaatttgcaaaaaaaaagaaagaaagg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttacaaaacataacagattgatcttaaggcataatctgcctttttcgatctctcttcatacgattttcaaaacgatttgtcatctttatctacgctaaattccgtaaatttgcaaaaaaaaagaaagaaagg Predict ORF larger than 30AA ================================================ Protein_Len: 34 Strand: + Start: 31 End: 132 .............................. M I C L F R S L F I R F S K R F V I F I Y A K F R K F A K K K K E R ttacaaaacataacagattgatcttaaggcataatctgcctttttcgatctctcttcatacgattttcaaaacgatttgtcatctttatctacgctaaattccgtaaatttgcaaaaaaaaagaaagaaagg 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================================================ ttacaaaacataacagattgatcttaaggcataatctgcctttttcgatctctcttcatacgattttcaaaacgatttgtcatctttatctacgctaaattccgtaaatttgcaaaaaaaaagaaagaaagg Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TF1529:TF1530|TF1529:TF1530:hypothetical protein:1-deoxyxylulose-5-phosphate synthase:->->:1634617..1634748 132 ttacaaaacataacagattgatcttaaggcataatctgcctttttcgatctctcttcatacgattttcaaaacgatttgtcatctttatctacgctaaattccgtaaatttgcaaaaaaaaagaaagaaagg Intra-Species Hit: Count: 1 Min: 1 Max: 113 Len: 113 Subject: tfor_TF1529_TF1530|hypothetical protein:1-deoxyxylulose-5-phosphate synthase|POSITIVE:POSITIVE|[1634617,1634748]|132 HSP 1 e-value: 6.0E-58 bit: 224.0 Len: 113 Query Start:1 Query End:113 Subject Strand: POSITIVE Subject Start: 1 Subject End: 113 ttacaaaacataacagattgatcttaaggcataatctgcctttttcgatctctcttcatacgattttcaaaacgatttgtcatctttatctacgctaaattccgtaaatttgc................... ttacaaaacataacagattgatcttaaggcataatctgcctttttcgatctctcttcatacgattttcaaaacgatttgtcatctttatctacgctaaattccgtaaatttgc................... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUACAAAACAUAACAGAUUGAUCUUAAGGCAUAAUCUGCCUUUUUCGAUCUCUCUUCAUACGAUUUUCAAAACGAUUUGUCAUCUUUAUCUACGCUAAAUUCCGUAAAUUUGC ((((..........(((((((....((((((.....))))))..)))))))..........(((..((.....))...)))......................))))...... (-18.00) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GCAAAUUUACGGAAUUUAGCGUAGAUAAAGAUGACAAAUCGUUUUGAAAAUCGUAUGAAGAGAGAUCGAAAAAGGCAGAUUAUGCCUUAAGAUCAAUCUGUUAUGUUUUGUAA ......(((((((((.((((...(((.(((((((....)))))))....)))......(((..((((....((((((.....))))))..))))..))))))).))))))))) (-27.80) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 291 82 42 226 193 tfor:TF0289|5end_conserved_hypothetical_protein_318015..318245_POSITIVE 290 59 20 212 168 tfor:TF1223|5end_conserved_hypothetical_protein_1309770..1310000_POSITIVE 266 63 23 60 24 tfor:TF3116|5end_conserved_hypothetical_protein_3352136..3352366_POSITIVE 258 74 35 211 176 tfor:TF1485|5end_conserved_hypothetical_protein_1581871..1582101_POSITIVE 247 104 64 174 129 tfor:TF0408|5end_possible_gliding_motility-related_lipoprotein_425777..426007_POSITIVE 246 80 36 209 159 tfor:TF2948|5end_2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxy_late_synthase_3154823..3155053_POSITIVE 245 110 73 50 7 tfor:TF0461|5end_ATP:cob(I)alamin_adenosyltransferase_476990..477220_POSITIVE 243 69 24 53 9 tfor:TF3045|5end_two-component_system_response_regulator_3273807..3274037_POSITIVE 243 62 28 106 72 tfor:TF2849|5end_histidinol-phosphate_transaminase_3037288..3037518_POSITIVE 241 76 33 123 71 tfor:TF1995|5end_exonuclease_2147148..2147378_POSITIVE 241 66 26 120 77 tfor:TF0906|5end_conserved_hypothetical_protein_949675..949905_POSITIVE 239 86 41 227 189 tfor:TF0332|5end_conserved_hypothetical_protein_359333..359563_POSITIVE 238 63 26 205 170 tfor:TF1628|5end_conserved_hypothetical_protein_1740627..1740857_POSITIVE 237 61 27 231 198 tfor:TF2945|5end_DNA-directed_RNA_polymerase_beta'_subunit_3147448..3147678_POSITIVE 236 64 28 208 170 tfor:TF0356|5end_transposase_element_373519..373749_POSITIVE 235 56 14 57 4 tfor:TF2800|5end_anti-sigma_factor_2985145..2985375_POSITIVE 235 95 51 214 168 tfor:TF2773|5end_S-adenosylmethionine_tRNA_ribosyltransferase_2958117..2958347_POSITIVE 233 53 13 105 63 tfor:TF2659|5end_conserved_hypothetical_protein_2832526..2832756_POSITIVE 233 73 37 59 33 tfor:TF0190|5end_cell_division_protein_FtsH_204029..204259_POSITIVE 232 60 18 79 36 tfor:TF1177|5end_conserved_hypothetical_protein;_possible_ribosomal_protein_S1_1261175..1261405_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 245 110 73 50 7 tfor:TF0460|3end_hypothetical_protein_477070..477220_POSITIVE 243 62 28 127 93 tfor:TF2848|3end_cobalamin_biosynthesis_protein_3037389..3037539_POSITIVE 241 76 33 123 71 tfor:TF1994|3end_acyl-CoA_synthetase_2147228..2147378_POSITIVE 236 64 28 96 58 tfor:TF0355|3end_transposase_element_373487..373637_POSITIVE 233 73 37 40 14 tfor:TF0189|3end_phosphatidate_cytidylytransferase_(CDP-diglyceride_synthetase)_204090..204240_POSITIVE 226 70 28 137 92 tfor:TF2641|3end_riboflavin_kinase/FAD_synthase_2810732..2810882_POSITIVE 224 60 11 73 22 tfor:TF2964|3end_type_I_restriction_enzyme_3176273..3176423_POSITIVE 221 94 51 42 4 tfor:TF0151|3end_hydrolase/beta-alanine_synthase_162072..162222_POSITIVE 220 83 42 83 38 tfor:TF2396|3end_dimethyladenosine_transferase_2568617..2568767_POSITIVE 219 80 34 109 55 tfor:TF1698|3end_mobilization_protein_1819782..1819932_POSITIVE 218 50 12 36 3 tfor:TF2430|3end_hypothetical_protein_2613204..2613354_POSITIVE 216 59 18 117 76 tfor:TF0439|3end_Na+-transporting_NADH:ubiquinone_oxidoreductase,_subunit_1_463689..463839_POSITIVE 215 57 14 58 7 tfor:TF2575|3end_methionine_aminopeptidase_2745985..2746135_POSITIVE 215 60 13 73 24 tfor:TF2180|3end_phosphoribosylamine--glycine_ligase_2353931..2354081_POSITIVE 215 51 15 76 40 tfor:TF1529|3end_hypothetical_protein_1634556..1634706_POSITIVE 212 69 22 77 38 tfor:TF1109|3end_lipoprotein_1179997..1180147_POSITIVE 211 69 22 63 2 tfor:TF2950|3end_chloromuconate_cycloisomerase_3158549..3158699_POSITIVE 211 82 48 133 97 tfor:TF2724|3end_anti-sigma_factor_2899448..2899598_POSITIVE 211 57 14 138 103 tfor:TF2098|3end_excinuclease_ABC,_subunit_C_2272942..2273092_POSITIVE 210 107 61 80 37 tfor:TF2707|3end_glutamine_amidotransferase_2880163..2880313_POSITIVE