Origin IGS: taacataagcatctattactgttaacaatggcggaacaacgcaatgtcgttccgccctttacagataccaaaacgccccttgcaaccgataaggcttgcaaggggcgtttgtttaaagctta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 taagctttaaacaaacgccccttgcaagccttatcggttgcaaggggcgttttggtatctgtaaagggcggaacgacattgcgttgttccgccattgttaacagtaatagatgcttatgtta Mask Tandem Repeat Region ================================================ taacataagcatctattactgttaacaatggcggaacaacgcaatgtcgttccgccctttacagataccaaaacgccccttgcaaccgataaggcttgcaaggggcgtttgtttaaagctta Find is-nt database================================================ Query_seq: PI0212:PI0213|PI0212:PI0213:surface protein/internalin-related protein:conserved hypothetical protein:->->:207083..207204 122 taacataagcatctattactgttaacaatggcggaacaacgcaatgtcgttccgccctttacagataccaaaacgccccttgcaaccgataaggcttgcaaggggcgtttgtttaaagctta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI0212:PI0213|PI0212:PI0213:surface protein/internalin-related protein:conserved hypothetical protein:->->:207083..207204 122 taacataagcatctattactgttaacaatggcggaacaacgcaatgtcgttccgccctttacagataccaaaacgccccttgcaaccgataaggcttgcaaggggcgtttgtttaaagctta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI0212:PI0213|PI0212:PI0213:surface protein/internalin-related protein:conserved hypothetical protein:->->:207083..207204 122 taacataagcatctattactgttaacaatggcggaacaacgcaatgtcgttccgccctttacagataccaaaacgccccttgcaaccgataaggcttgcaaggggcgtttgtttaaagctta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taacataagcatctattactgttaacaatggcggaacaacgcaatgtcgttccgccctttacagataccaaaacgccccttgcaaccgataaggcttgcaaggggcgtttgtttaaagctta Predict ORF larger than 30AA ================================================ Protein_Len: 34 Strand: + Start: 19 End: 120 .................. M L T M A E Q R N V V P P F T D T K T P L A T D K A C K G R L F K A .. Protein_Len: 33 Strand: - Start: 3 End: 101 .. C L C R N S N V I A S C R L T T G G K V S V L V G R A V S L A Q M ..................... taacataagcatctattactgttaacaatggcggaacaacgcaatgtcgttccgccctttacagataccaaaacgccccttgcaaccgataaggcttgcaaggggcgtttgtttaaagctta 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================================================ taacataagcatctattactgttaacaatggcggaacaacgcaatgtcgttccgccctttacagataccaaaacgccccttgcaaccgataaggcttgcaaggggcgtttgtttaaagctta Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 83 HP_score: -11.0 Tail_Score: -3.63991 Start: 29 End: 57 Full_Region: tttggtatctgtaaa gggcggaacgac attgc gttgttccgcca ttgttaacagtaata ............................gggcggaacgacattgcgttgttccgcca................................................................. TransTerm Strand: - Conf: 87 HP_score: -14.5 Tail_Score: -2.78073 Start: 30 End: 56 Full_Region: ttggtatctgtaaag ggcggaacgac attgc gttgttccgcc attgttaacagtaat .............................ggcggaacgacattgcgttgttccgcc.................................................................. TransTerm Strand: + Conf: 100 HP_score: -15.3 Tail_Score: -3.25603 Start: 75 End: 106 Full_Region: TACAGATACCAAAAC GCCCCTTGCAACC GATAA GGCTTGCAAGGGGC GTTTGTTTAAAGCTT ..........................................................................GCCCCTTGCAACCGATAAGGCTTGCAAGGGGC................ Find igs database================================================ Query_seq: PI0212:PI0213|PI0212:PI0213:surface protein/internalin-related protein:conserved hypothetical protein:->->:207083..207204 122 taacataagcatctattactgttaacaatggcggaacaacgcaatgtcgttccgccctttacagataccaaaacgccccttgcaaccgataaggcttgcaaggggcgtttgtttaaagctta Intra-Species Hit: Count: 1 Min: 1 Max: 122 Len: 122 Subject: pint_PI0212_PI0213|surface protein/internalin-related protein:conserved hypothetical protein|POSITIVE:POSITIVE|[207083,207204]|122 HSP 1 e-value: 2.0E-63 bit: 242.0 Len: 122 Query Start:1 Query End:122 Subject Strand: POSITIVE Subject Start: 1 Subject End: 122 taacataagcatctattactgttaacaatggcggaacaacgcaatgtcgttccgccctttacagataccaaaacgccccttgcaaccgataaggcttgcaaggggcgtttgtttaaagctta taacataagcatctattactgttaacaatggcggaacaacgcaatgtcgttccgccctttacagataccaaaacgccccttgcaaccgataaggcttgcaaggggcgtttgtttaaagctta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAACAUAAGCAUCUAUUACUGUUAACAAUGGCGGAACAACGCAAUGUCGUUCCGCCCUUUACAGAUACCAAAACGCCCCUUGCAACCGAUAAGGCUUGCAAGGGGCGUUUGUUUAAAGCUUA .....(((((........((((.......((((((((.((.....)).))))))))....))))......(((((((((((((((((.....)).))))))))))))))).......))))) (-53.20) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAGCUUUAAACAAACGCCCCUUGCAAGCCUUAUCGGUUGCAAGGGGCGUUUUGGUAUCUGUAAAGGGCGGAACGACAUUGCGUUGUUCCGCCAUUGUUAACAGUAAUAGAUGCUUAUGUUA ..(((.......(((((((((((((((.((.....))))))))))))))))).(((((((((....(((((((((((.....))))))))))).(((....)))..)))))))))...))). (-57.50) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 365 108 61 203 155 pint:PI0269|5end_conserved_hypothetical_protein_259835..260065_POSITIVE 350 113 72 192 146 pint:PI0585|5end_conserved_hypothetical_protein_532660..532890_POSITIVE 344 113 75 231 196 pint:PI0380|5end_conserved_hypothetical_protein_350162..350392_POSITIVE 333 119 75 229 169 pint:PI1528|5end_hypothetical_protein_1449685..1449915_POSITIVE 331 64 29 72 35 pint:PI2100|5end_conserved_hypothetical_protein_2053351..2053581_POSITIVE 331 108 68 64 25 pint:PI1600|5end_conserved_hypothetical_protein_1529269..1529499_POSITIVE 330 90 41 91 46 pint:PI2017|5end_conserved_hypothetical_protein_1974862..1975092_POSITIVE 323 100 53 144 95 pint:PI1784|5end_possible_dTDP-glucose_4,6-dehydratase,_NAD-dependent_epimerase/dehydratase_family_1716201..1716431_POSITIVE 315 119 78 60 5 pint:PI1571|5end_surface_antigen_BspA_1494765..1494995_POSITIVE 313 106 67 228 184 pint:PI0806|5end_heavy_metal_efflux_pump_743679..743909_POSITIVE 313 56 29 213 185 pint:PI0739|5end_conserved_hypothetical_protein_671794..672024_POSITIVE 311 109 68 191 150 pint:PI2131|5end_hypothetical_protein_2080678..2080908_POSITIVE 311 117 74 73 22 pint:PI2086|5end_signal_peptidase_I_2041835..2042065_POSITIVE 311 110 62 196 139 pint:PI1626|5end_hypothetical_protein_1550194..1550424_POSITIVE 311 107 63 134 75 pint:PI1136|5end_conserved_hypothetical_protein_1062195..1062425_POSITIVE 310 118 73 188 136 pint:PI1223|5end_conserved_hypothetical_protein_1143537..1143767_POSITIVE 310 107 69 208 168 pint:PI0595|5end_conserved_hypothetical_protein_545571..545801_POSITIVE 309 107 66 62 21 pint:PI1811|5end_conserved_hypothetical_protein_1749518..1749748_POSITIVE 309 110 71 159 133 pint:PI0756|5end_50S_ribosomal_protein_L7/L12_687146..687376_POSITIVE 308 120 75 140 95 pint:PI1639|5end_conserved_hypothetical_protein_1556725..1556955_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 382 109 65 53 9 pint:PI0927|3end_transglutaminase-related_protein_859696..859846_POSITIVE 365 108 61 78 30 pint:PI0268|3end_lysozyme-related_protein_259790..259940_POSITIVE 362 107 64 68 16 pint:PI0156|3end_conserved_hypothetical_protein_150913..151063_POSITIVE 355 110 61 55 4 pint:PI1012|3end_DNA-binding_protein,_histone-like_family_933544..933694_POSITIVE 340 80 32 79 40 pint:PI0005|3end_hypothetical_protein_7450..7600_POSITIVE 330 90 41 82 37 pint:PI2016|3end_ribosomal_large_subunit_pseudouridine_synthase_D_1974933..1975083_POSITIVE 311 109 68 144 103 pint:PI2130|3end_DNA_polymerase_I_2080711..2080861_POSITIVE 311 107 63 62 3 pint:PI1135|3end_hypothetical_protein_1062203..1062353_POSITIVE 307 114 75 63 22 pint:PI1777|3end_conserved_hypothetical_protein_1710081..1710231_POSITIVE 303 99 51 131 74 pint:PI1265|3end_hypothetical_protein_1185512..1185662_POSITIVE 300 90 41 123 67 pint:PI1065|3end_hypothetical_protein_983650..983800_POSITIVE 290 70 28 70 35 pint:PI2168|3end_hypothetical_protein_2111746..2111896_POSITIVE 290 108 61 106 55 pint:PI0201|3end_hypothetical_protein_195398..195548_POSITIVE 284 65 26 100 53 pint:PI0092|3end_regulatory_protein_RecX_89651..89801_POSITIVE 283 89 41 146 99 pint:PI0196|3end_hypothetical_protein_188643..188793_POSITIVE 280 109 61 56 13 pint:PI1338|3end_phosphoserine_phosphatase_1256594..1256744_POSITIVE 279 98 53 75 36 pint:PI0634|3end_conserved_hypothetical_protein_581121..581271_POSITIVE 278 119 73 54 10 pint:PI1479|3end_xanthine_phosphoribosyltransferase_1402747..1402897_POSITIVE 278 113 71 69 23 pint:PI0220|3end_conserved_hypothetical_protein_212341..212491_POSITIVE 277 109 67 60 3 pint:PI1706|3end_GTP-binding_protein_1623668..1623818_POSITIVE