Origin IGS: actgatatttcttttctaaaatcttataattaaatgccgaaagagcttgtacgaagcatcgaagttatgttcgtttacccaacaatgcagcccttatgcttttgaatttcaaaaatactaattttatgaataaccgccaaacgattggcaaaatatcttccatgacagcgtttcgacagaatacatttatttacaaagctacacttctta .........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 taagaagtgtagctttgtaaataaatgtattctgtcgaaacgctgtcatggaagatattttgccaatcgtttggcggttattcataaaattagtatttttgaaattcaaaagcataagggctgcattgttgggtaaacgaacataacttcgatgcttcgtacaagctctttcggcatttaattataagattttagaaaagaaatatcagt Mask Tandem Repeat Region ================================================ actgatatttcttttctaaaatcttataattaaatgccgaaagagcttgtacgaagcatcgaagttatgttcgtttacccaacaatgcagcccttatgcttttgaatttcaaaaatactaattttatgaataaccgccaaacgattggcaaaatatcttccatgacagcgtttcgacagaatacatttatttacaaagctacacttctta Find is-nt database================================================ Query_seq: PI1383:PI1384|PI1383:PI1384:biopolymer transport protein tolQ related:conserved hypothetical protein:->->:1305101..1305310 210 actgatatttcttttctaaaatcttataattaaatgccgaaagagcttgtacgaagcatcgaagttatgttcgtttacccaacaatgcagcccttatgcttttgaatttcaaaaatactaattttatgaataaccgccaaacgattggcaaaatatcttccatgacagcgtttcgacagaatacatttatttacaaagctacacttctta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI1383:PI1384|PI1383:PI1384:biopolymer transport protein tolQ related:conserved hypothetical protein:->->:1305101..1305310 210 actgatatttcttttctaaaatcttataattaaatgccgaaagagcttgtacgaagcatcgaagttatgttcgtttacccaacaatgcagcccttatgcttttgaatttcaaaaatactaattttatgaataaccgccaaacgattggcaaaatatcttccatgacagcgtttcgacagaatacatttatttacaaagctacacttctta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI1383:PI1384|PI1383:PI1384:biopolymer transport protein tolQ related:conserved hypothetical protein:->->:1305101..1305310 210 actgatatttcttttctaaaatcttataattaaatgccgaaagagcttgtacgaagcatcgaagttatgttcgtttacccaacaatgcagcccttatgcttttgaatttcaaaaatactaattttatgaataaccgccaaacgattggcaaaatatcttccatgacagcgtttcgacagaatacatttatttacaaagctacacttctta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 actgatatttcttttctaaaatcttataattaaatgccgaaagagcttgtacgaagcatcgaagttatgttcgtttacccaacaatgcagcccttatgcttttgaatttcaaaaatactaattttatgaataaccgccaaacgattggcaaaatatcttccatgacagcgtttcgacagaatacatttatttacaaagctacacttctta Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: + Start: 26 End: 118 ......................... M I K C R K S L Y E A S K L C S F T Q Q C S P Y A F E F Q K Y ............................................................................................ Protein_Len: 38 Strand: + Start: 96 End: 209 ............................................................................................... M L L N F K N T N F M N N R Q T I G K I S S M T A F R Q N T F I Y K A T L L . Protein_Len: 35 Strand: - Start: 78 End: 182 ............................................................................. G V I C G K H K Q I E F I S I K H I V A L R N A F Y R G H C R K S L M ............................ Protein_Len: 41 Strand: - Start: 68 End: 190 ................................................................... T R K G L L A A R I S K F K L F V L K I F L R W V I P L I D E M V A N R C F V N M .................... actgatatttcttttctaaaatcttataattaaatgccgaaagagcttgtacgaagcatcgaagttatgttcgtttacccaacaatgcagcccttatgcttttgaatttcaaaaatactaattttatgaataaccgccaaacgattggcaaaatatcttccatgacagcgtttcgacagaatacatttatttacaaagctacacttctta 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: 1 End: 30 ACTGATATTTCTTTTCTAAAATCTTATAAT.................................................................................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ actgatatttcttttctaaaatcttataattaaatgccgaaagagcttgtacgaagcatcgaagttatgttcgtttacccaacaatgcagcccttatgcttttgaatttcaaaaatactaattttatgaataaccgccaaacgattggcaaaatatcttccatgacagcgtttcgacagaatacatttatttacaaagctacacttctta Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 47 HP_score: -2.4 Tail_Score: -3.53444 Start: 60 End: 73 Full_Region: GCTTGTACGAAGCAT CGAA GTTATG TTCG TTTACCCAACAATGC ...........................................................CGAAGTTATGTTCG......................................................................................................................................... Find igs database================================================ Query_seq: PI1383:PI1384|PI1383:PI1384:biopolymer transport protein tolQ related:conserved hypothetical protein:->->:1305101..1305310 210 actgatatttcttttctaaaatcttataattaaatgccgaaagagcttgtacgaagcatcgaagttatgttcgtttacccaacaatgcagcccttatgcttttgaatttcaaaaatactaattttatgaataaccgccaaacgattggcaaaatatcttccatgacagcgtttcgacagaatacatttatttacaaagctacacttctta Intra-Species Hit: Count: 1 Min: 1 Max: 210 Len: 210 Subject: pint_PI1383_PI1384|biopolymer transport protein tolQ related:conserved hypothetical protein|POSITIVE:POSITIVE|[1305101,1305310]|210 HSP 1 e-value: 1.0E-115 bit: 416.0 Len: 210 Query Start:1 Query End:210 Subject Strand: POSITIVE Subject Start: 1 Subject End: 210 actgatatttcttttctaaaatcttataattaaatgccgaaagagcttgtacgaagcatcgaagttatgttcgtttacccaacaatgcagcccttatgcttttgaatttcaaaaatactaattttatgaataaccgccaaacgattggcaaaatatcttccatgacagcgtttcgacagaatacatttatttacaaagctacacttctta actgatatttcttttctaaaatcttataattaaatgccgaaagagcttgtacgaagcatcgaagttatgttcgtttacccaacaatgcagcccttatgcttttgaatttcaaaaatactaattttatgaataaccgccaaacgattggcaaaatatcttccatgacagcgtttcgacagaatacatttatttacaaagctacacttctta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACUGAUAUUUCUUUUCUAAAAUCUUAUAAUUAAAUGCCGAAAGAGCUUGUACGAAGCAUCGAAGUUAUGUUCGUUUACCCAACAAUGCAGCCCUUAUGCUUUUGAAUUUCAAAAAUACUAAUUUUAUGAAUAACCGCCAAACGAUUGGCAAAAUAUCUUCCAUGACAGCGUUUCGACAGAAUACAUUUAUUUACAAAGCUACACUUCUUA ..........................(((.((((((.(....)...((((.((((((...(..((((((.............(((.(((.......)))..)))...(((((((((....))))).)))).....(((((....)))))...........))))))..)))))))))))....)))))).)))................. (-28.50) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAGAAGUGUAGCUUUGUAAAUAAAUGUAUUCUGUCGAAACGCUGUCAUGGAAGAUAUUUUGCCAAUCGUUUGGCGGUUAUUCAUAAAAUUAGUAUUUUUGAAAUUCAAAAGCAUAAGGGCUGCAUUGUUGGGUAAACGAACAUAACUUCGAUGCUUCGUACAAGCUCUUUCGGCAUUUAAUUAUAAGAUUUUAGAAAAGAAAUAUCAGU ......(((((((((((..((((....))))....))))..)))).)))....(((((((((((((....))))).....(((.(((((((.....(((((.....)))))((..(((((((....((((.(.....).))))......(((....)))....)))))))...))............))))))))))..))))))))... (-39.20) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 310 95 55 124 77 pint:PI0824|5end_large_conductance_mechanosensitive_channel_protein_763337..763567_POSITIVE 305 177 136 85 43 pint:PI1139|5end_endopeptidase,_endothelin-converting_enzyme_1065216..1065446_POSITIVE 303 95 53 86 37 pint:PI0938|5end_hypothetical_protein_869345..869575_POSITIVE 297 79 35 204 164 pint:PI2099|5end_D-alanyl-D-alanine_dipeptidase_2052409..2052639_POSITIVE 297 76 35 107 59 pint:PI0037|5end_hypothetical_protein_39354..39584_POSITIVE 290 97 53 152 106 pint:PI1637|5end_hypothetical_protein_1554500..1554730_POSITIVE 290 80 31 190 143 pint:PI0930|5end_alpha-L-fucosidase_precursor_860977..861207_POSITIVE 281 80 35 60 8 pint:PI2141|5end_hypothetical_protein_2087169..2087399_POSITIVE 279 99 51 187 134 pint:PI0277|5end_hypothetical_protein_264980..265210_POSITIVE 273 179 135 186 148 pint:PI1653|5end_hypothetical_protein_1565158..1565388_POSITIVE 273 79 33 62 22 pint:PI1501|5end_GTP-binding_elongation_factor_family_protein_TypA/BipA_1421424..1421654_POSITIVE 269 98 53 56 11 pint:PI1405|5end_conserved_hypothetical_protein_1326035..1326265_POSITIVE 265 90 41 82 29 pint:PI0627|5end_conserved_hypothetical_protein_575618..575848_POSITIVE 264 176 135 69 28 pint:PI2020|5end_glycosyl_transferase,_group_2_family_protein_1976866..1977096_POSITIVE 262 87 44 199 144 pint:PI0754|5end_possible_outer_membrane_receptor_683771..684001_POSITIVE 262 179 135 205 154 pint:PI0285|5end_succinyltransferase_protein_270097..270327_POSITIVE 261 72 35 81 22 pint:PI2159|5end_immunoreactive_84_kDa_antigen_PG93_2105267..2105497_POSITIVE 261 64 34 73 33 pint:PI0751|5end_conserved_hypothetical_protein_680623..680853_POSITIVE 261 177 132 110 54 pint:PI0388|5end_integrase_354927..355157_POSITIVE 260 73 33 60 14 pint:PI1086|5end_pyruvate:ferredoxin_oxidoreductase_1006602..1006832_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 303 95 53 125 76 pint:PI0936|3end_conserved_hypothetical_protein_869464..869614_POSITIVE 279 99 51 148 95 pint:PI0276|3end_anti-restriction_protein_265021..265171_POSITIVE 266 99 54 147 102 pint:PI0488|3end_conserved_hypothetical_protein_447537..447687_POSITIVE 265 90 41 82 29 pint:PI0626|3end_penicillin-binding_protein,_D-alanyl-D-alanine_carboxypeptidase_575698..575848_POSITIVE 263 79 42 104 61 pint:PI0377|3end_DNA_primase/mobilizable_transposon,_excision_protein_347823..347973_POSITIVE 261 72 35 81 22 pint:PI2158|3end_glycosyl_transferase,_group_2_family_protein_2105347..2105497_POSITIVE 259 76 35 57 9 pint:PI0574|3end_hypothetical_protein_519444..519594_POSITIVE 255 91 51 72 36 pint:PI0706|3end_pyridoxal_phosphate_biosynthetic_protein_(4-hydroxythreonine-4-phosphate_dehydrogenase)_643394..643544_POSITIVE 253 74 34 75 27 pint:PI0092|3end_regulatory_protein_RecX_89651..89801_POSITIVE 252 99 51 147 98 pint:PI0023|3end_internalin-related_protein_28070..28220_POSITIVE 251 96 52 68 13 pint:PI1884|3end_conserved_hypothetical_protein_1827457..1827607_POSITIVE 251 180 136 99 51 pint:PI0605|3end_chloromuconate_cycloisomerase_553026..553176_POSITIVE 245 73 35 137 92 pint:PI0819|3end_hypothetical_protein_759919..760069_POSITIVE 244 78 36 136 101 pint:PI0579|3end_hypothetical_protein_524209..524359_POSITIVE 239 90 45 132 78 pint:PI1665|3end_thymidylate_synthase_1578804..1578954_POSITIVE 239 90 42 113 60 pint:PI0183|3end_hypothetical_protein_174810..174960_POSITIVE 238 190 142 108 57 pint:PI1943|3end_hypothetical_protein_1902206..1902356_POSITIVE 238 98 55 64 19 pint:PI0027|3end_aminopeptidase_C_31756..31906_POSITIVE 235 65 34 31 1 pint:PI1642|3end_conserved_hypothetical_protein_1560439..1560589_POSITIVE 235 65 34 31 1 pint:PI0348|3end_conserved_hypothetical_protein_323211..323361_POSITIVE