Origin IGS: tgatcagagaaatatctaaaacgcccaaggtagccctgtgccgtgaatgtcatggcacgggcttccaaaaggtaagtatagacgggacacagacacatgtccggtgtccccagtgtgagggaagcggcagggtgctggtgagttgcaagatgagccttgacatccgcccgtatagaaacagtcaacaatcctaacaaatcccacagct .........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 agctgtgggatttgttaggattgttgactgtttctatacgggcggatgtcaaggctcatcttgcaactcaccagcaccctgccgcttccctcacactggggacaccggacatgtgtctgtgtcccgtctatacttaccttttggaagcccgtgccatgacattcacggcacagggctaccttgggcgttttagatatttctctgatca Mask Tandem Repeat Region ================================================ tgatcagagaaatatctaaaacgcccaaggtagccctgtgccgtgaatgtcatggcacgggcttccaaaaggtaagtatagacgggacacagacacatgtccggtgtccccagtgtgagggaagcggcagggtgctggtgagttgcaagatgagccttgacatccgcccgtatagaaacagtcaacaatcctaacaaatcccacagct Find is-nt database================================================ Query_seq: PI1634:PI1635|PI1634:PI1635:conserved hypothetical protein:hypothetical protein:->->:1553880..1554087 208 tgatcagagaaatatctaaaacgcccaaggtagccctgtgccgtgaatgtcatggcacgggcttccaaaaggtaagtatagacgggacacagacacatgtccggtgtccccagtgtgagggaagcggcagggtgctggtgagttgcaagatgagccttgacatccgcccgtatagaaacagtcaacaatcctaacaaatcccacagct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI1634:PI1635|PI1634:PI1635:conserved hypothetical protein:hypothetical protein:->->:1553880..1554087 208 tgatcagagaaatatctaaaacgcccaaggtagccctgtgccgtgaatgtcatggcacgggcttccaaaaggtaagtatagacgggacacagacacatgtccggtgtccccagtgtgagggaagcggcagggtgctggtgagttgcaagatgagccttgacatccgcccgtatagaaacagtcaacaatcctaacaaatcccacagct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI1634:PI1635|PI1634:PI1635:conserved hypothetical protein:hypothetical protein:->->:1553880..1554087 208 tgatcagagaaatatctaaaacgcccaaggtagccctgtgccgtgaatgtcatggcacgggcttccaaaaggtaagtatagacgggacacagacacatgtccggtgtccccagtgtgagggaagcggcagggtgctggtgagttgcaagatgagccttgacatccgcccgtatagaaacagtcaacaatcctaacaaatcccacagct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tgatcagagaaatatctaaaacgcccaaggtagccctgtgccgtgaatgtcatggcacgggcttccaaaaggtaagtatagacgggacacagacacatgtccggtgtccccagtgtgagggaagcggcagggtgctggtgagttgcaagatgagccttgacatccgcccgtatagaaacagtcaacaatcctaacaaatcccacagct Predict ORF larger than 30AA ================================================ Protein_Len: 60 Strand: + Start: 3 End: 191 .. M R E I S K T P K V A L C R E C H G T G F Q K V S I D G T Q T H V R C P Q C E G S G R V L V S C K M S L D I R P Y R N S ................. Protein_Len: 43 Strand: - Start: 53 End: 181 .................................................... P V P K W F T L I S P V C V C T R H G W H S P L P L T S T L Q L I L R S M R G Y L F M ........................... Protein_Len: 60 Strand: - Start: 19 End: 204 .................. W P L G T G H I D H C P S G F P L Y L R S V S V H G T D G T H P F R C P A P S N C S S G Q C G G T Y F C D V I R V F G M .... Protein_Len: 60 Strand: - Start: 3 End: 206 .. L Y G Q A T F T M A R A E L L Y T Y V P C L C M D P T G L T L S A A P H Q H T A L H A K V D A R I S V T L L G L L D W M .. tgatcagagaaatatctaaaacgcccaaggtagccctgtgccgtgaatgtcatggcacgggcttccaaaaggtaagtatagacgggacacagacacatgtccggtgtccccagtgtgagggaagcggcagggtgctggtgagttgcaagatgagccttgacatccgcccgtatagaaacagtcaacaatcctaacaaatcccacagct 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================================================ tgatcagagaaatatctaaaacgcccaaggtagccctgtgccgtgaatgtcatggcacgggcttccaaaaggtaagtatagacgggacacagacacatgtccggtgtccccagtgtgagggaagcggcagggtgctggtgagttgcaagatgagccttgacatccgcccgtatagaaacagtcaacaatcctaacaaatcccacagct Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 75 HP_score: -12.9 Tail_Score: -2.54655 Start: 33 End: 62 Full_Region: acttaccttttggaa gcccgtgccatga cat tcacggcacagggc taccttgggcgtttt ................................gcccgtgccatgacattcacggcacagggc.................................................................................................................................................. Find igs database================================================ Query_seq: PI1634:PI1635|PI1634:PI1635:conserved hypothetical protein:hypothetical protein:->->:1553880..1554087 208 tgatcagagaaatatctaaaacgcccaaggtagccctgtgccgtgaatgtcatggcacgggcttccaaaaggtaagtatagacgggacacagacacatgtccggtgtccccagtgtgagggaagcggcagggtgctggtgagttgcaagatgagccttgacatccgcccgtatagaaacagtcaacaatcctaacaaatcccacagct Intra-Species Hit: Count: 1 Min: 1 Max: 208 Len: 208 Subject: pint_PI1634_PI1635|conserved hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[1553880,1554087]|208 HSP 1 e-value: 1.0E-114 bit: 412.0 Len: 208 Query Start:1 Query End:208 Subject Strand: POSITIVE Subject Start: 1 Subject End: 208 tgatcagagaaatatctaaaacgcccaaggtagccctgtgccgtgaatgtcatggcacgggcttccaaaaggtaagtatagacgggacacagacacatgtccggtgtccccagtgtgagggaagcggcagggtgctggtgagttgcaagatgagccttgacatccgcccgtatagaaacagtcaacaatcctaacaaatcccacagct tgatcagagaaatatctaaaacgcccaaggtagccctgtgccgtgaatgtcatggcacgggcttccaaaaggtaagtatagacgggacacagacacatgtccggtgtccccagtgtgagggaagcggcagggtgctggtgagttgcaagatgagccttgacatccgcccgtatagaaacagtcaacaatcctaacaaatcccacagct Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGAUCAGAGAAAUAUCUAAAACGCCCAAGGUAGCCCUGUGCCGUGAAUGUCAUGGCACGGGCUUCCAAAAGGUAAGUAUAGACGGGACACAGACACAUGUCCGGUGUCCCCAGUGUGAGGGAAGCGGCAGGGUGCUGGUGAGUUGCAAGAUGAGCCUUGACAUCCGCCCGUAUAGAAACAGUCAACAAUCCUAACAAAUCCCACAGCU .....(((......)))...((((....((.(((((.((((((((.....))))))))))))).)).................(((((((.(((....)))..)))))))..))))..((((.((((..((((((.(((..(((....)))..)))..).)))))..))))...((.....))...............))))...... (-69.60) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGCUGUGGGAUUUGUUAGGAUUGUUGACUGUUUCUAUACGGGCGGAUGUCAAGGCUCAUCUUGCAACUCACCAGCACCCUGCCGCUUCCCUCACACUGGGGACACCGGACAUGUGUCUGUGUCCCGUCUAUACUUACCUUUUGGAAGCCCGUGCCAUGACAUUCACGGCACAGGGCUACCUUGGGCGUUUUAGAUAUUUCUCUGAUCA .(.((.((((..((.((((..(((((.((((......))))(((((((........)))).))).......))))).)))).))..)))).)))....(((((((.((((....)))))))))))...........(((...((.((((((((((.((.....)).))))).))))).))..)))....(((((......)))))... (-71.30) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 542 128 83 221 175 pint:PI0356|5end_hypothetical_protein_326642..326872_POSITIVE 447 72 33 229 181 pint:PI0333|5end_hypothetical_protein_313478..313708_POSITIVE 419 145 101 83 36 pint:PI0128|5end_dipeptidase,_pathogenicity_island-encoded_protein_D_120532..120762_POSITIVE 389 167 121 95 35 pint:PI1664|5end_conserved_hypothetical_protein_1577285..1577515_POSITIVE 387 170 124 196 131 pint:PI1947|5end_hypothetical_protein_1902534..1902764_POSITIVE 387 68 21 223 176 pint:PI0330|5end_hypothetical_protein_310447..310677_POSITIVE 386 159 113 206 158 pint:PI0051|5end_hypothetical_protein_52607..52837_POSITIVE 379 129 84 60 11 pint:PI0265|5end_conjugative_transposon_protein,_TraO_257296..257526_POSITIVE 376 138 91 62 6 pint:PI1588|5end_DNA_polymerase_III,_epsilon_chain_1516302..1516532_POSITIVE 373 67 22 87 34 pint:PI1609|5end_Na+/H+_anti-porter_1536058..1536288_POSITIVE 371 156 112 80 23 pint:PI1757|5end_hypothetical_protein_1683934..1684164_POSITIVE 371 167 121 95 35 pint:PI0370|5end_conserved_hypothetical_protein_340453..340683_POSITIVE 369 147 101 224 163 pint:PI1365|5end_conserved_hypothetical_protein;_probable_transmembrane_protein_1283976..1284206_POSITIVE 367 169 123 107 50 pint:PI0126|5end_conserved_hypothetical_protein_117925..118155_POSITIVE 366 70 22 214 172 pint:PI0034|5end_FKBP-type_peptidyl-prolyl_cis-trans_isomerase_37151..37381_POSITIVE 364 72 36 229 177 pint:PI1626|5end_hypothetical_protein_1550194..1550424_POSITIVE 364 150 106 231 168 pint:PI0427|5end_conserved_hypothetical_protein_391140..391370_POSITIVE 360 149 101 59 4 pint:PI1672|5end_conserved_hypothetical_protein;_possible_DNA-binding_protein,_histone-like_family_1587027..1587257_POSITIVE 360 129 83 228 176 pint:PI1531|5end_biotin--acetyl-CoA-carboxylase_ligase_1450839..1451069_POSITIVE 357 170 123 196 144 pint:PI0171|5end_hypothetical_protein_163850..164080_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 501 66 29 62 25 pint:PI1634|3end_conserved_hypothetical_protein_1553819..1553969_POSITIVE 406 155 111 119 75 pint:PI2129|3end_octaprenyl-diphosphate_synthase_2077721..2077871_POSITIVE 389 167 121 77 17 pint:PI1663|3end_hypothetical_protein_1577347..1577497_POSITIVE 388 170 122 122 47 pint:PI0906|3end_hypothetical_protein_836008..836158_POSITIVE 379 129 84 55 6 pint:PI0264|3end_transfer_region-related_protein,_TraN_257371..257521_POSITIVE 373 168 121 121 55 pint:PI1741|3end_lipid-A-disaccharide_synthase_1663856..1664006_POSITIVE 371 156 112 123 66 pint:PI1758|3end_hypothetical_protein_1684057..1684207_POSITIVE 366 146 101 104 59 pint:PI1227|3end_conserved_hypothetical_protein;_possible_DNA-binding_protein,_histone-like_family_1148974..1149124_POSITIVE 366 70 22 84 42 pint:PI0033|3end_peptidylprolyl_isomerase_37101..37251_POSITIVE 359 73 33 87 50 pint:PI0340|3end_conserved_hypothetical_protein_316735..316885_POSITIVE 352 170 125 142 77 pint:PI2074|3end_conserved_hypothetical_protein_2034375..2034525_POSITIVE 352 146 101 56 7 pint:PI1783|3end_possible_4-diphosphocytidyl-2c-methyl-D-erythritol_synthase_1716158..1716308_POSITIVE 350 150 102 109 46 pint:PI1488|3end_hypothetical_protein_1407829..1407979_POSITIVE 347 160 111 106 53 pint:PI1954|3end_translation_initiation_factor_IF-2_1911647..1911797_POSITIVE 347 132 102 47 10 pint:PI1402|3end_3-deoxy-7-phosphoheptulonate_synthase_1323980..1324130_POSITIVE 345 144 102 79 37 pint:PI2157|3end_xanthosine_triphosphate_pyrophosphatase,_HAM1_family_2104457..2104607_POSITIVE 336 68 22 138 84 pint:PI0998|3end_possible_flavin_reductase_domain_protein_923336..923486_POSITIVE 336 170 123 76 25 pint:PI0363|3end_hypothetical_protein_333760..333910_POSITIVE 334 69 25 70 25 pint:PI1353|3end_conserved_hypothetical_protein_1270932..1271082_POSITIVE 331 169 126 81 28 pint:PI1265|3end_hypothetical_protein_1185512..1185662_POSITIVE