Origin IGS: attcttttttgtttaaatcttccgtgatatgcgtgcaaagatacaaaaaactcgttacttacaactgcctgctactaactttttcgtacctttgcagtatgaaaataggaattattgtggcaatggacaaggagtttacgcagctcaagtccattctcgaacatacggaaacg .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 cgtttccgtatgttcgagaatggacttgagctgcgtaaactccttgtccattgccacaataattcctattttcatactgcaaaggtacgaaaaagttagtagcaggcagttgtaagtaacgagttttttgtatctttgcacgcatatcacggaagatttaaacaaaaaagaat Mask Tandem Repeat Region ================================================ attcttttttgtttaaatcttccgtgatatgcgtgcaaagatacaaaaaactcgttacttacaactgcctgctactaactttttcgtacctttgcagtatgaaaataggaattattgtggcaatggacaaggagtttacgcagctcaagtccattctcgaacatacggaaacg Find is-nt database================================================ Query_seq: PI1495:PI1496|PI1495:PI1496:conserved hypothetical protein:nucleoside phosphorylase:->->:1417083..1417255 173 attcttttttgtttaaatcttccgtgatatgcgtgcaaagatacaaaaaactcgttacttacaactgcctgctactaactttttcgtacctttgcagtatgaaaataggaattattgtggcaatggacaaggagtttacgcagctcaagtccattctcgaacatacggaaacg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI1495:PI1496|PI1495:PI1496:conserved hypothetical protein:nucleoside phosphorylase:->->:1417083..1417255 173 attcttttttgtttaaatcttccgtgatatgcgtgcaaagatacaaaaaactcgttacttacaactgcctgctactaactttttcgtacctttgcagtatgaaaataggaattattgtggcaatggacaaggagtttacgcagctcaagtccattctcgaacatacggaaacg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI1495:PI1496|PI1495:PI1496:conserved hypothetical protein:nucleoside phosphorylase:->->:1417083..1417255 173 attcttttttgtttaaatcttccgtgatatgcgtgcaaagatacaaaaaactcgttacttacaactgcctgctactaactttttcgtacctttgcagtatgaaaataggaattattgtggcaatggacaaggagtttacgcagctcaagtccattctcgaacatacggaaacg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 attcttttttgtttaaatcttccgtgatatgcgtgcaaagatacaaaaaactcgttacttacaactgcctgctactaactttttcgtacctttgcagtatgaaaataggaattattgtggcaatggacaaggagtttacgcagctcaagtccattctcgaacatacggaaacg Predict ORF larger than 30AA ================================================ Protein_Len: 52 Strand: + Start: 17 End: 172 ................ M F R D M R A K I Q K T R Y L Q L P A T N F F V P L Q Y E N R N Y C G N G Q G V Y A A Q V H S R T Y G N . Protein_Len: 55 Strand: + Start: 9 End: 173 ........ M F K S S V I C V Q R Y K K L V T Y N C L L L T F S Y L C S M K I G I I V A M D K E F T Q L K S I L E H T E T Protein_Len: 31 Strand: - Start: 62 End: 154 ............................................................. L Q R S S V K E Y R Q L I F I P I I T A I S L S N V C S L D M ................... attcttttttgtttaaatcttccgtgatatgcgtgcaaagatacaaaaaactcgttacttacaactgcctgctactaactttttcgtacctttgcagtatgaaaataggaattattgtggcaatggacaaggagtttacgcagctcaagtccattctcgaacatacggaaacg 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================================================ attcttttttgtttaaatcttccgtgatatgcgtgcaaagatacaaaaaactcgttacttacaactgcctgctactaactttttcgtacctttgcagtatgaaaataggaattattgtggcaatggacaaggagtttacgcagctcaagtccattctcgaacatacggaaacg Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PI1495:PI1496|PI1495:PI1496:conserved hypothetical protein:nucleoside phosphorylase:->->:1417083..1417255 173 attcttttttgtttaaatcttccgtgatatgcgtgcaaagatacaaaaaactcgttacttacaactgcctgctactaactttttcgtacctttgcagtatgaaaataggaattattgtggcaatggacaaggagtttacgcagctcaagtccattctcgaacatacggaaacg Intra-Species Hit: Count: 1 Min: 1 Max: 173 Len: 173 Subject: pint_PI1495_PI1496|conserved hypothetical protein:nucleoside phosphorylase|POSITIVE:POSITIVE|[1417083,1417255]|173 HSP 1 e-value: 1.0E-93 bit: 343.0 Len: 173 Query Start:1 Query End:173 Subject Strand: POSITIVE Subject Start: 1 Subject End: 173 attcttttttgtttaaatcttccgtgatatgcgtgcaaagatacaaaaaactcgttacttacaactgcctgctactaactttttcgtacctttgcagtatgaaaataggaattattgtggcaatggacaaggagtttacgcagctcaagtccattctcgaacatacggaaacg attcttttttgtttaaatcttccgtgatatgcgtgcaaagatacaaaaaactcgttacttacaactgcctgctactaactttttcgtacctttgcagtatgaaaataggaattattgtggcaatggacaaggagtttacgcagctcaagtccattctcgaacatacggaaacg Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUUCUUUUUUGUUUAAAUCUUCCGUGAUAUGCGUGCAAAGAUACAAAAAACUCGUUACUUACAACUGCCUGCUACUAACUUUUUCGUACCUUUGCAGUAUGAAAAUAGGAAUUAUUGUGGCAAUGGACAAGGAGUUUACGCAGCUCAAGUCCAUUCUCGAACAUACGGAAACG ...................(((((((.(((((.(((((((.(((.(((((...((((.(..((......))..).))))))))).))).))))))))))))................(((.(((((((...(((((.....)))))..))))))).)))....)))))))... (-39.00) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CGUUUCCGUAUGUUCGAGAAUGGACUUGAGCUGCGUAAACUCCUUGUCCAUUGCCACAAUAAUUCCUAUUUUCAUACUGCAAAGGUACGAAAAAGUUAGUAGCAGGCAGUUGUAAGUAACGAGUUUUUUGUAUCUUUGCACGCAUAUCACGGAAGAUUUAAACAAAAAAGAAU ..(((((((((((.((..(((((((..(((.........)))...)))))))..........................((((((((((((((((.((.((.((..((....))..)).)))).)))))))))))))))).)).)))).))))))).................. (-45.10) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 348 123 82 188 139 pint:PI1753|5end_conserved_hypothetical_protein_1680291..1680521_POSITIVE 304 129 81 166 113 pint:PI0684|5end_coproporphyrinogen_III_oxidase_619357..619587_POSITIVE 304 129 81 101 48 pint:PI0683|5end_hypothetical_protein_619292..619522_POSITIVE 294 111 86 226 201 pint:PI2038|5end_conserved_hypothetical_protein;_possible_internalin-related_protein_1990463..1990693_POSITIVE 283 130 81 123 67 pint:PI0761|5end_hypothetical_protein_696173..696403_POSITIVE 281 76 31 142 96 pint:PI2146|5end_prolipoprotein_diacylglyceryl_transferase_2092402..2092632_POSITIVE 281 168 121 89 53 pint:PI1727|5end__ATP-dependent_Clp_protease,_ATP-binding_subunit_1645680..1645910_POSITIVE 278 150 108 227 174 pint:PI2032|5end_RNA_polymerase_sigma_factor,_ECF_subfamily_1986544..1986774_POSITIVE 277 97 53 69 21 pint:PI0473|5end_30S_ribosomal_protein_S14_438634..438864_POSITIVE 275 168 124 144 100 pint:PI0128|5end_dipeptidase,_pathogenicity_island-encoded_protein_D_120532..120762_POSITIVE 274 158 115 144 106 pint:PI0064|5end_hypothetical_protein_63622..63852_POSITIVE 273 110 66 187 149 pint:PI0950|5end_50S_ribosomal_protein_L31_883327..883557_POSITIVE 272 70 24 91 47 pint:PI1311|5end_large_protein_related_to_C.hutchinsonii_large_proteins_1226625..1226855_POSITIVE 270 166 127 206 173 pint:PI0226|5end_ABC_transporter,_ATP-binding_/_permease_protein_222110..222340_POSITIVE 270 166 127 134 101 pint:PI0225|5end_conserved_hypothetical_protein_222038..222268_POSITIVE 267 170 126 51 2 pint:PI1644|5end_hypothetical_protein_1560372..1560602_POSITIVE 267 157 113 51 6 pint:PI1366|5end_conserved_hypothetical_protein;_possible_hydrolase,_HAD_superfamily_1286046..1286276_POSITIVE 265 136 91 161 109 pint:PI0895|5end_2-oxoglutarate_oxidoreductase,_beta_subunit,_possible_ketoisovalerate_oxidoreductase,__vorA_826347..826577_POSITIVE 263 88 51 147 106 pint:PI2074|5end_conserved_hypothetical_protein_2033660..2033890_POSITIVE 263 169 122 154 94 pint:PI1196|5end_hypothetical_protein_1113401..1113631_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 348 123 82 97 48 pint:PI1751|3end_desulfoferrodoxin_1680280..1680430_POSITIVE 310 127 81 101 57 pint:PI0807|3end_hydrolase,_haloacid_dehalogenase-like_hydrolase_745278..745428_POSITIVE 304 129 81 101 48 pint:PI0682|3end_hypothetical_protein_619372..619522_POSITIVE 302 80 34 53 7 pint:PI1610|3end_Na+/H+_anti-porter_1538002..1538152_POSITIVE 294 111 86 52 27 pint:PI2037|3end_TIM-barrel_protein,_NifR3_family_1990369..1990519_POSITIVE 282 158 116 112 64 pint:PI0010|3end_conserved_hypothetical_protein_11679..11829_POSITIVE 277 97 53 60 12 pint:PI0472|3end_50S_ribosomal_protein_L5_438705..438855_POSITIVE 274 158 115 62 24 pint:PI0063|3end_transcriptional_regulator,_GntR_family_63620..63770_POSITIVE 273 110 66 59 21 pint:PI0949|3end_endonuclease_883279..883429_POSITIVE 272 110 69 44 4 pint:PI0107|3end_2-methylthioadenine_synthetase_104652..104802_POSITIVE 270 160 117 43 1 pint:PI0479|3end_50S_ribosomal_protein_L15_441648..441798_POSITIVE 265 136 91 84 32 pint:PI0894|3end_2-oxoglutarate_oxidoreductase,_gamma_subunit_(2-oxoglutarate-ferredoxin_oxidoreductase)_826350..826500_POSITIVE 265 159 111 138 85 pint:PI0125|3end_undecaprenyl_pyrophosphate_synthase_117890..118040_POSITIVE 263 169 122 133 73 pint:PI1195|3end_hypothetical_protein_1113460..1113610_POSITIVE 258 59 19 71 34 pint:PI1730|3end_hypothetical_protein_1650367..1650517_POSITIVE 257 67 24 100 57 pint:PI0117|3end_ribonuclease_HI_111314..111464_POSITIVE 256 167 123 124 80 pint:PI1710|3end_ABC-type_permease_component_1627356..1627506_POSITIVE 255 66 21 73 27 pint:PI0706|3end_pyridoxal_phosphate_biosynthetic_protein_(4-hydroxythreonine-4-phosphate_dehydrogenase)_643394..643544_POSITIVE 250 123 81 76 18 pint:PI1919|3end_2,3-bisphosphoglycerate-independent_phosphoglycerate_mutase_1863875..1864025_POSITIVE 250 156 116 103 70 pint:PI0024|3end_hypothetical_protein_28559..28709_POSITIVE