Origin IGS: tgatctataagaatagaatttgttctcacaaaaaaatggaataaaccgtaattgcagaaagaatcagttatatagacaaatccatttgagaacaagagcaaaagataaaatatatagaacgattaaagatatctttgtgttaaattttattagcagttaaagataatggtaaattaaaattatt .........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 aataattttaatttaccattatctttaactgctaataaaatttaacacaaagatatctttaatcgttctatatattttatcttttgctcttgttctcaaatggatttgtctatataactgattctttctgcaattacggtttattccatttttttgtgagaacaaattctattcttatagatca Mask Tandem Repeat Region ================================================ tgatctataagaatagaatttgttctcacaaaaaaatggaataaaccgtaattgcagaaagaatcagttatatagacaaatccatttgagaacaagagcaaaagataaaatatatagaacgattaaagatatctttgtgttaaattttattagcagttaaagataatggtaaattaaaattatt Find is-nt database================================================ Query_seq: PI0514:PI0515|PI0514:PI0515:possible cell filamentation protein:conserved hypothetical protein:->->:473001..473184 184 tgatctataagaatagaatttgttctcacaaaaaaatggaataaaccgtaattgcagaaagaatcagttatatagacaaatccatttgagaacaagagcaaaagataaaatatatagaacgattaaagatatctttgtgttaaattttattagcagttaaagataatggtaaattaaaattatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI0514:PI0515|PI0514:PI0515:possible cell filamentation protein:conserved hypothetical protein:->->:473001..473184 184 tgatctataagaatagaatttgttctcacaaaaaaatggaataaaccgtaattgcagaaagaatcagttatatagacaaatccatttgagaacaagagcaaaagataaaatatatagaacgattaaagatatctttgtgttaaattttattagcagttaaagataatggtaaattaaaattatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI0514:PI0515|PI0514:PI0515:possible cell filamentation protein:conserved hypothetical protein:->->:473001..473184 184 tgatctataagaatagaatttgttctcacaaaaaaatggaataaaccgtaattgcagaaagaatcagttatatagacaaatccatttgagaacaagagcaaaagataaaatatatagaacgattaaagatatctttgtgttaaattttattagcagttaaagataatggtaaattaaaattatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tgatctataagaatagaatttgttctcacaaaaaaatggaataaaccgtaattgcagaaagaatcagttatatagacaaatccatttgagaacaagagcaaaagataaaatatatagaacgattaaagatatctttgtgttaaattttattagcagttaaagataatggtaaattaaaattatt Predict ORF larger than 30AA ================================================ Protein_Len: 46 Strand: + Start: 20 End: 157 ................... M F S Q K N G I N R N C R K N Q L Y R Q I H L R T R A K D K I Y R T I K D I F V L N F I S S ........................... Protein_Len: 30 Strand: - Start: 67 End: 156 .................................................................. N Y L C I W K L V L A F S L I Y L V I L S I K T N F K I L M ............................ Protein_Len: 37 Strand: - Start: 3 End: 113 .. D I L I S N T R V F F H F L G Y N C F S D T I Y V F G N S F L L L L Y F M ....................................................................... tgatctataagaatagaatttgttctcacaaaaaaatggaataaaccgtaattgcagaaagaatcagttatatagacaaatccatttgagaacaagagcaaaagataaaatatatagaacgattaaagatatctttgtgttaaattttattagcagttaaagataatggtaaattaaaattatt 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: 83 Start: 144 End: 173 ...............................................................................................................................................TTTACCATTATCTTTAACTGCTAATAAAAT........... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tgatctataagaatagaatttgttctcacaaaaaaatggaataaaccgtaattgcagaaagaatcagttatatagacaaatccatttgagaacaagagcaaaagataaaatatatagaacgattaaagatatctttgtgttaaattttattagcagttaaagataatggtaaattaaaattatt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PI0514:PI0515|PI0514:PI0515:possible cell filamentation protein:conserved hypothetical protein:->->:473001..473184 184 tgatctataagaatagaatttgttctcacaaaaaaatggaataaaccgtaattgcagaaagaatcagttatatagacaaatccatttgagaacaagagcaaaagataaaatatatagaacgattaaagatatctttgtgttaaattttattagcagttaaagataatggtaaattaaaattatt Intra-Species Hit: Count: 1 Min: 1 Max: 184 Len: 184 Subject: pint_PI0514_PI0515|possible cell filamentation protein:conserved hypothetical protein|POSITIVE:POSITIVE|[473001,473184]|184 HSP 1 e-value: 1.0E-87 bit: 323.0 Len: 184 Query Start:1 Query End:184 Subject Strand: POSITIVE Subject Start: 1 Subject End: 184 tgatctataagaatagaatttgttctcacnnnnnnntggaataaaccgtaattgcagaaagaatcagttatatagacaaatccatttgagaacaagagcaaaagataaaatatatagaacgattaaagatatctttgtgttaaattttattagcagttaaagataatggtaaattaaaattatt tgatctataagaatagaatttgttctcacaaaaaaatggaataaaccgtaattgcagaaagaatcagttatatagacaaatccatttgagaacaagagcaaaagataaaatatatagaacgattaaagatatctttgtgttaaattttattagcagttaaagataatggtaaattaaaattatt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGAUCUAUAAGAAUAGAAUUUGUUCUCACAAAAAAAUGGAAUAAACCGUAAUUGCAGAAAGAAUCAGUUAUAUAGACAAAUCCAUUUGAGAACAAGAGCAAAAGAUAAAAUAUAUAGAACGAUUAAAGAUAUCUUUGUGUUAAAUUUUAUUAGCAGUUAAAGAUAAUGGUAAAUUAAAAUUAUU ...(((((....))))).((((((((((......((((((.......(((((((..........))))))).........)))))))))))))))).................................((((((((((((((......))))))..))))))))................... (-27.89) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUAAUUUUAAUUUACCAUUAUCUUUAACUGCUAAUAAAAUUUAACACAAAGAUAUCUUUAAUCGUUCUAUAUAUUUUAUCUUUUGCUCUUGUUCUCAAAUGGAUUUGUCUAUAUAACUGAUUCUUUCUGCAAUUACGGUUUAUUCCAUUUUUUUGUGAGAACAAAUUCUAUUCUUAUAGAUCA ...................(((((((...((.(((......))).)).))))))).........(.((((((..........((((.(((..(....(((((((.....(..((.....((.....))......))..).....)))))))....)..))).)))).........)))))).). (-22.71) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 253 130 87 152 100 pint:PI1471|5end_conserved_hypothetical_protein_1395050..1395280_POSITIVE 253 130 87 118 66 pint:PI1469|5end_hypothetical_protein_1395016..1395246_POSITIVE 222 170 136 111 81 pint:PI1134|5end_ABC_transporter,_ATP-binding_protein_1060374..1060604_POSITIVE 219 87 52 150 104 pint:PI0801|5end_hypothetical_protein_739365..739595_POSITIVE 217 127 88 213 171 pint:PI0807|5end_hydrolase,_haloacid_dehalogenase-like_hydrolase_744407..744637_POSITIVE 212 90 42 132 92 pint:PI1152|5end_response_regulator/transcriptional_regulator_RprY_1076372..1076602_POSITIVE 210 98 57 125 83 pint:PI1026|5end_uridine_phosphorylase_942300..942530_POSITIVE 209 89 47 75 32 pint:PI1362|5end_60Kd_inner_membrane_protein_1279820..1280050_POSITIVE 201 100 65 188 157 pint:PI0478|5end_50S_ribosomal_protein_L30_440923..441153_POSITIVE 199 68 39 218 192 pint:PI0906|5end_hypothetical_protein_835653..835883_POSITIVE 197 57 36 105 83 pint:PI0932|5end_conserved_hypothetical_protein;_possible_hemin_receptor_863854..864084_POSITIVE 197 100 52 221 183 pint:PI0740|5end_hypothetical_protein_672112..672342_POSITIVE 197 77 38 135 88 pint:PI0555|5end_conserved_hypothetical_protein_504577..504807_POSITIVE 194 90 46 197 160 pint:PI0231|5end_transcriptional_regulator_229453..229683_POSITIVE 193 86 45 108 61 pint:PI1224|5end_sensor_histidine_kinase_and_response_regulator_1144574..1144804_POSITIVE 192 83 42 222 187 pint:PI0810|5end_hypothetical_protein_746743..746973_POSITIVE 192 83 42 217 182 pint:PI0811|5end_protease/hemagglutinin_PrtT,_streptopain_family_746738..746968_POSITIVE 192 83 42 109 74 pint:PI0809|5end_hypothetical_protein_746630..746860_POSITIVE 192 106 64 157 117 pint:PI0178|5end_2-oxoglutarate_synthase,_subunit_korA_169524..169754_POSITIVE 191 68 45 56 26 pint:PI2066|5end_hypothetical_protein_2027179..2027409_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 253 130 87 144 92 pint:PI1470|3end_hypothetical_protein_1395122..1395272_POSITIVE 222 170 136 61 31 pint:PI1133|3end_GrpE_protein_1060404..1060554_POSITIVE 218 64 36 92 65 pint:PI0914|3end_ATPase,_AAA_family_844992..845142_POSITIVE 217 127 88 120 78 pint:PI0806|3end_heavy_metal_efflux_pump_744394..744544_POSITIVE 212 90 42 62 22 pint:PI1151|3end_hypothetical_protein_1076382..1076532_POSITIVE 212 70 21 142 85 pint:PI0023|3end_internalin-related_protein_28070..28220_POSITIVE 209 89 47 68 25 pint:PI1361|3end_CTP_synthase_(UTP-ammonia_lyase)_1279893..1280043_POSITIVE 209 155 114 64 28 pint:PI0413|3end_outer_membrane_protein_384019..384169_POSITIVE 198 68 21 141 92 pint:PI0770|3end_hypothetical_protein_706354..706504_POSITIVE 197 77 38 77 30 pint:PI0554|3end_hypothetical_protein_504599..504749_POSITIVE 194 90 46 68 31 pint:PI0229|3end_hypothetical_protein_229404..229554_POSITIVE 192 106 64 136 96 pint:PI0177|3end_2-oxoglutarate_synthase,_subunit_korB_169583..169733_POSITIVE 191 68 45 50 20 pint:PI2065|3end_hypothetical_protein_2027253..2027403_POSITIVE 191 155 116 58 20 pint:PI1288|3end_hypothetical_protein_1202829..1202979_POSITIVE 188 119 75 91 51 pint:PI2015|3end_D-alanine--D-alanine_ligase_1973796..1973946_POSITIVE 188 98 53 145 94 pint:PI0320|3end_probable_cobalamin_adenosyltransferase_302652..302802_POSITIVE 187 170 134 141 103 pint:PI1324|3end_conserved_hypothetical_protein_1243025..1243175_POSITIVE 187 94 54 59 15 pint:PI1275|3end_indole-3-glycerol_phosphate_synthase_1194307..1194457_POSITIVE 185 89 48 91 52 pint:PI1159|3end_1,4-alpha-glucan_branching_enzyme,_N-terminal_region_1084757..1084907_POSITIVE 184 120 72 81 30 pint:PI1589|3end_conserved_hypothetical_protein_1517842..1517992_POSITIVE