Origin IGS: aatcgtattcttttaaagagtttttaatttgtttgtattggtatagacgtaagttattgcgattttgtggcaaagaaaataagaaaaaatactttttatttgattttttctttattgcagtttataaaaaccatacttgagatgccgcacgggcatctcaagccattgtta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 taacaatggcttgagatgcccgtgcggcatctcaagtatggtttttataaactgcaataaagaaaaaatcaaataaaaagtattttttcttattttctttgccacaaaatcgcaataacttacgtctataccaatacaaacaaattaaaaactctttaaaagaatacgatt Mask Tandem Repeat Region ================================================ aatcgtattcttttaaagagtttttaatttgtttgtattggtatagacgtaagttattgcgattttgtggcaaagaaaataagaaaaaatactttttatttgattttttctttattgcagtttataaaaaccatacttgagatgccgcacgggcatctcaagccattgtta Find is-nt database================================================ Query_seq: PI2034:PI2035|PI2034:PI2035:conserved hypothetical protein:Holliday junction DNA helicase ruvB:->->:1988181..1988351 171 aatcgtattcttttaaagagtttttaatttgtttgtattggtatagacgtaagttattgcgattttgtggcaaagaaaataagaaaaaatactttttatttgattttttctttattgcagtttataaaaaccatacttgagatgccgcacgggcatctcaagccattgtta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI2034:PI2035|PI2034:PI2035:conserved hypothetical protein:Holliday junction DNA helicase ruvB:->->:1988181..1988351 171 aatcgtattcttttaaagagtttttaatttgtttgtattggtatagacgtaagttattgcgattttgtggcaaagaaaataagaaaaaatactttttatttgattttttctttattgcagtttataaaaaccatacttgagatgccgcacgggcatctcaagccattgtta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI2034:PI2035|PI2034:PI2035:conserved hypothetical protein:Holliday junction DNA helicase ruvB:->->:1988181..1988351 171 aatcgtattcttttaaagagtttttaatttgtttgtattggtatagacgtaagttattgcgattttgtggcaaagaaaataagaaaaaatactttttatttgattttttctttattgcagtttataaaaaccatacttgagatgccgcacgggcatctcaagccattgtta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aatcgtattcttttaaagagtttttaatttgtttgtattggtatagacgtaagttattgcgattttgtggcaaagaaaataagaaaaaatactttttatttgattttttctttattgcagtttataaaaaccatacttgagatgccgcacgggcatctcaagccattgtta Predict ORF larger than 30AA ================================================ Protein_Len: 37 Strand: + Start: 27 End: 137 .......................... M C L Y W Y R R K L L R F C G K E N K K K Y F L F D F F F I A V Y K N H T .................................. Protein_Len: 45 Strand: + Start: 37 End: 171 .................................... M G I D V S Y C D F V A K K I R K N T F Y L I F S L L Q F I K T I L E M P H G H L K P L L Protein_Len: 38 Strand: - Start: 2 End: 115 . D Y E K L S N K I Q K Y Q Y L R L N N R N Q P L S F L F F Y K K N S K K K M ........................................................ aatcgtattcttttaaagagtttttaatttgtttgtattggtatagacgtaagttattgcgattttgtggcaaagaaaataagaaaaaatactttttatttgattttttctttattgcagtttataaaaaccatacttgagatgccgcacgggcatctcaagccattgtta 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: 99 End: 128 ..................................................................................................TTTGATTTTTTCTTTATTGCAGTTTATAAA........................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aatcgtattcttttaaagagtttttaatttgtttgtattggtatagacgtaagttattgcgattttgtggcaaagaaaataagaaaaaatactttttatttgattttttctttattgcagtttataaaaaccatacttgagatgccgcacgggcatctcaagccattgtta Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PI2034:PI2035|PI2034:PI2035:conserved hypothetical protein:Holliday junction DNA helicase ruvB:->->:1988181..1988351 171 aatcgtattcttttaaagagtttttaatttgtttgtattggtatagacgtaagttattgcgattttgtggcaaagaaaataagaaaaaatactttttatttgattttttctttattgcagtttataaaaaccatacttgagatgccgcacgggcatctcaagccattgtta Intra-Species Hit: Count: 1 Min: 1 Max: 171 Len: 171 Subject: pint_PI2034_PI2035|conserved hypothetical protein:Holliday junction DNA helicase ruvB|POSITIVE:POSITIVE|[1988181,1988351]|171 HSP 1 e-value: 3.0E-45 bit: 182.0 Len: 92 Query Start:1 Query End:92 Subject Strand: POSITIVE Subject Start: 1 Subject End: 92 aatcgtattcttttaaagagtttttaatttgtttgtattggtatagacgtaagttattgcgattttgtggcaaagaaaataagaaaaaatac............................................................................... aatcgtattcttttaaagagtttttaatttgtttgtattggtatagacgtaagttattgcgattttgtggcaaagaaaataagaaaaaatac............................................................................... HSP 2 e-value: 2.0E-27 bit: 123.0 Len: 62 Query Start:110 Query End:171 Subject Strand: POSITIVE Subject Start: 110 Subject End: 171 .............................................................................................................ctttattgcagtttataaaaaccatacttgagatgccgcacgggcatctcaagccattgtta .............................................................................................................ctttattgcagtttataaaaaccatacttgagatgccgcacgggcatctcaagccattgtta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUCGUAUUCUUUUAAAGAGUUUUUAAUUUGUUUGUAUUGGUAUAGACGUAAGUUAUUGCGAUUUUGUGGCAAAGAAAAUAAGAAAAAAUACUUUUUAUUUGAUUUUUUCUUUAUUGCAGUUUAUAAAAACCAUACUUGAGAUGCCGCACGGGCAUCUCAAGCCAUUGUUA .................(.(((((((....(((((((....))))))).......((((((((...(..(.(((..(((((((((.......)))))))))..))))..)...))))))))...))))))))...(((((((((((.....)))))))))))......... (-38.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAACAAUGGCUUGAGAUGCCCGUGCGGCAUCUCAAGUAUGGUUUUUAUAAACUGCAAUAAAGAAAAAAUCAAAUAAAAAGUAUUUUUUCUUAUUUUCUUUGCCACAAAAUCGCAAUAACUUACGUCUAUACCAAUACAAACAAAUUAAAAACUCUUUAAAAGAAUACGAUU ........((((((((((((.....))))))))))))..((((((((............(((((((((((.........).)))))))))).......((((.........))))..............................)))))))).................. (-31.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 339 164 131 43 5 pint:PI0260|5end_conjugative_transposon_protein,_TraJ_253023..253253_POSITIVE 329 168 130 46 3 pint:PI1430|5end_subtilisin-like_serine_proteinase_1349598..1349828_POSITIVE 302 75 31 76 32 pint:PI0861|5end_glucosamine--fructose-6-phosphate_aminotransferase_(glutamine-fructose-6-phosphate_transaminase_(isomerizing))_796346..796576_POSITIVE 296 164 131 223 181 pint:PI1981|5end_hypothetical_protein_1937897..1938127_POSITIVE 295 149 101 177 136 pint:PI0068|5end_arginine_repressor_66586..66816_POSITIVE 287 164 138 216 180 pint:PI0338|5end_hypothetical_protein_315337..315567_POSITIVE 284 168 131 225 173 pint:PI1327|5end_conserved_hypothetical_protein_1245563..1245793_POSITIVE 280 159 111 161 115 pint:PI0635|5end_dephospho-CoA_kinase_580954..581184_POSITIVE 277 72 31 44 10 pint:PI1319|5end_possible_OmpA_,_outer_membrane_protein-related_protein_1235655..1235885_POSITIVE 277 164 143 53 32 pint:PI0139|5end_pyridoxine_biosynthesis_protein_131835..132065_POSITIVE 274 169 129 36 3 pint:PI2112|5end_phosphopantetheine_adenylyltransferase_2063194..2063424_POSITIVE 267 61 28 173 143 pint:PI1831|5end_conserved_hypothetical_protein_1770298..1770528_POSITIVE 265 165 144 231 205 pint:PI2138|5end_nicotinate_phosphoribosyltransferase_2083836..2084066_POSITIVE 263 169 132 60 7 pint:PI1735|5end_conserved_hypothetical_protein_1653428..1653658_POSITIVE 261 158 111 54 12 pint:PI0576|5end_helicase,_UvrD/Rep_520226..520456_POSITIVE 255 165 130 87 52 pint:PI1642|5end_conserved_hypothetical_protein_1558800..1559030_POSITIVE 253 169 131 94 47 pint:PI0587|5end_conserved_hypothetical_protein_534416..534646_POSITIVE 251 165 123 196 157 pint:PI1224|5end_sensor_histidine_kinase_and_response_regulator_1144574..1144804_POSITIVE 249 152 111 97 52 pint:PI1311|5end_large_protein_related_to_C.hutchinsonii_large_proteins_1226625..1226855_POSITIVE 248 170 130 226 191 pint:PI2155|5end_hypothetical_protein_2100664..2100894_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 295 149 101 97 56 pint:PI0067|3end_hypothetical_protein_66586..66736_POSITIVE 276 75 37 40 6 pint:PI0825|3end_hypothetical_protein_764196..764346_POSITIVE 265 165 144 122 96 pint:PI2137|3end_RNA_methylase_SpoU_family_2083807..2083957_POSITIVE 255 165 130 90 55 pint:PI1641|3end_hypothetical_protein_1558883..1559033_POSITIVE 249 168 128 80 34 pint:PI1807|3end_hypothetical_protein_1742481..1742631_POSITIVE 247 155 111 66 19 pint:PI0732|3end_conserved_hypothetical_protein_664367..664517_POSITIVE 240 74 37 59 16 pint:PI1829|3end_hypothetical_protein_1769439..1769589_POSITIVE 239 167 140 63 37 pint:PI0145|3end_secDF_export_membrane_protein_139724..139874_POSITIVE 238 170 144 34 4 pint:PI1603|3end_hypothetical_protein_1534005..1534155_POSITIVE 237 159 115 65 28 pint:PI0838|3end_DNA_replication_and_repair_protein_773927..774077_POSITIVE 236 160 117 121 72 pint:PI0345|3end_conserved_hypothetical_protein_320809..320959_POSITIVE 235 170 124 135 100 pint:PI1801|3end_30S_ribosomal_protein_S9_1734412..1734562_POSITIVE 233 165 130 56 8 pint:PI1605|3end_conserved_hypothetical_protein_1535178..1535328_POSITIVE 232 168 122 50 3 pint:PI1723|3end_conserved_hypothetical_protein_1642133..1642283_POSITIVE 232 168 133 146 97 pint:PI0816|3end_glycogen_debranching_enzyme_756920..757070_POSITIVE 229 170 128 118 79 pint:PI1559|3end_hypothetical_protein_1476972..1477122_POSITIVE 229 168 139 144 115 pint:PI1078|3end_conserved_hypothetical_protein_999930..1000080_POSITIVE 228 155 130 142 112 pint:PI1864|3end_chromate_transport_protein_1811009..1811159_POSITIVE 228 169 124 151 103 pint:PI1619|3end_two-component_system_response_regulator_1544018..1544168_POSITIVE 228 163 131 55 20 pint:PI0948|3end_hypothetical_protein_881978..882128_POSITIVE