Origin IGS: tgctacaaagttacattaaaaggtgtgaatgcccaaaatatttcaccatttttttgcttattgcgagccttgcaatgcattctatccataataagaaataaatcagaatactttaaaaatccttgtatgttcgttaaactatatgaaaagaaagaataaaatcgtctatttagataaatgttaccgacgagtaacttatctttgcggttacttgttggtaacattaagtaa .........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 ttacttaatgttaccaacaagtaaccgcaaagataagttactcgtcggtaacatttatctaaatagacgattttattctttcttttcatatagtttaacgaacatacaaggatttttaaagtattctgatttatttcttattatggatagaatgcattgcaaggctcgcaataagcaaaaaaatggtgaaatattttgggcattcacaccttttaatgtaactttgtagca Mask Tandem Repeat Region ================================================ tgctacaaagttacattaaaaggtgtgaatgcccaaaatatttcaccatttttttgcttattgcgagccttgcaatgcattctatccataataagaaataaatcagaatactttaaaaatccttgtatgttcgttaaactatatgaaaagaaagaataaaatcgtctatttagataaatgttaccgacgagtaacttatctttgcggttacttgttggtaacattaagtaa Find is-nt database================================================ Query_seq: PI0557:PI0558|PI0557:PI0558:conserved hypothetical protein:probable transcriptional regulator, TetR family:->->:506945..507175 231 tgctacaaagttacattaaaaggtgtgaatgcccaaaatatttcaccatttttttgcttattgcgagccttgcaatgcattctatccataataagaaataaatcagaatactttaaaaatccttgtatgttcgttaaactatatgaaaagaaagaataaaatcgtctatttagataaatgttaccgacgagtaacttatctttgcggttacttgttggtaacattaagtaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI0557:PI0558|PI0557:PI0558:conserved hypothetical protein:probable transcriptional regulator, TetR family:->->:506945..507175 231 tgctacaaagttacattaaaaggtgtgaatgcccaaaatatttcaccatttttttgcttattgcgagccttgcaatgcattctatccataataagaaataaatcagaatactttaaaaatccttgtatgttcgttaaactatatgaaaagaaagaataaaatcgtctatttagataaatgttaccgacgagtaacttatctttgcggttacttgttggtaacattaagtaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI0557:PI0558|PI0557:PI0558:conserved hypothetical protein:probable transcriptional regulator, TetR family:->->:506945..507175 231 tgctacaaagttacattaaaaggtgtgaatgcccaaaatatttcaccatttttttgcttattgcgagccttgcaatgcattctatccataataagaaataaatcagaatactttaaaaatccttgtatgttcgttaaactatatgaaaagaaagaataaaatcgtctatttagataaatgttaccgacgagtaacttatctttgcggttacttgttggtaacattaagtaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tgctacaaagttacattaaaaggtgtgaatgcccaaaatatttcaccatttttttgcttattgcgagccttgcaatgcattctatccataataagaaataaatcagaatactttaaaaatccttgtatgttcgttaaactatatgaaaagaaagaataaaatcgtctatttagataaatgttaccgacgagtaacttatctttgcggttacttgttggtaacattaagtaa Predict ORF larger than 30AA ================================================ Protein_Len: 44 Strand: + Start: 25 End: 156 ........................ M N A Q N I S P F F C L L R A L Q C I L S I I R N K S E Y F K N P C M F V K L Y E K K E ........................................................................... Protein_Len: 44 Strand: + Start: 98 End: 229 ................................................................................................. M N Q N T L K I L V C S L N Y M K R K N K I V Y L D K C Y R R V T Y L C G Y L L V T L S .. Protein_Len: 32 Strand: - Start: 14 End: 109 ............. M L L H S H G F Y K V M K K S I A L R A I C E I W L L F Y I L M .......................................................................................................................... Protein_Len: 60 Strand: - Start: 6 End: 224 ..... G N K Q K N R A K C H M R D M I L F L D S Y K L F G Q I N T L S Y S F F S Y F R R N L Y I N G V L L K D K R N S T P L M ....... tgctacaaagttacattaaaaggtgtgaatgcccaaaatatttcaccatttttttgcttattgcgagccttgcaatgcattctatccataataagaaataaatcagaatactttaaaaatccttgtatgttcgttaaactatatgaaaagaaagaataaaatcgtctatttagataaatgttaccgacgagtaacttatctttgcggttacttgttggtaacattaagtaa 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: 111 End: 140 ..............................................................................................................CTTTAAAAATCCTTGTATGTTCGTTAAACT........................................................................................... PromScan Matrix: RpoD-17 Strand: - Score: 81 Start: 88 End: 117 .......................................................................................TTTAAAGTATTCTGATTTATTTCTTATTAT.................................................................................................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tgctacaaagttacattaaaaggtgtgaatgcccaaaatatttcaccatttttttgcttattgcgagccttgcaatgcattctatccataataagaaataaatcagaatactttaaaaatccttgtatgttcgttaaactatatgaaaagaaagaataaaatcgtctatttagataaatgttaccgacgagtaacttatctttgcggttacttgttggtaacattaagtaa Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PI0557:PI0558|PI0557:PI0558:conserved hypothetical protein:probable transcriptional regulator, TetR family:->->:506945..507175 231 tgctacaaagttacattaaaaggtgtgaatgcccaaaatatttcaccatttttttgcttattgcgagccttgcaatgcattctatccataataagaaataaatcagaatactttaaaaatccttgtatgttcgttaaactatatgaaaagaaagaataaaatcgtctatttagataaatgttaccgacgagtaacttatctttgcggttacttgttggtaacattaagtaa Intra-Species Hit: Count: 1 Min: 1 Max: 231 Len: 231 Subject: pint_PI0557_PI0558|conserved hypothetical protein:probable transcriptional regulator, TetR family|POSITIVE:POSITIVE|[506945,507175]|231 HSP 1 e-value: 1.0E-115 bit: 416.0 Len: 231 Query Start:1 Query End:231 Subject Strand: POSITIVE Subject Start: 1 Subject End: 231 tgctacaaagttacattaaaaggtgtgaatgcccaaaatatttcaccannnnnnngcttattgcgagccttgcaatgcattctatccataataagaaataaatcagaatactttaaaaatccttgtatgttcgttaaactatatgaaaagaaagaataaaatcgtctatttagataaatgttaccgacgagtaacttatctttgcggttacttgttggtaacattaagtaa tgctacaaagttacattaaaaggtgtgaatgcccaaaatatttcaccatttttttgcttattgcgagccttgcaatgcattctatccataataagaaataaatcagaatactttaaaaatccttgtatgttcgttaaactatatgaaaagaaagaataaaatcgtctatttagataaatgttaccgacgagtaacttatctttgcggttacttgttggtaacattaagtaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGCUACAAAGUUACAUUAAAAGGUGUGAAUGCCCAAAAUAUUUCACCAUUUUUUUGCUUAUUGCGAGCCUUGCAAUGCAUUCUAUCCAUAAUAAGAAAUAAAUCAGAAUACUUUAAAAAUCCUUGUAUGUUCGUUAAACUAUAUGAAAAGAAAGAAUAAAAUCGUCUAUUUAGAUAAAUGUUACCGACGAGUAACUUAUCUUUGCGGUUACUUGUUGGUAACAUUAAGUAA ((((..(((((..........((...((((((.(((((.............)))))...(((((((...)))))))))))))...)).......((......)).....))))).......(((.....(((((........)))))....))).........((((....)))).((((((((((((((((((((.........)))))))))))))))))))).)))). (-46.82) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUACUUAAUGUUACCAACAAGUAACCGCAAAGAUAAGUUACUCGUCGGUAACAUUUAUCUAAAUAGACGAUUUUAUUCUUUCUUUUCAUAUAGUUUAACGAACAUACAAGGAUUUUUAAAGUAUUCUGAUUUAUUUCUUAUUAUGGAUAGAAUGCAUUGCAAGGCUCGCAAUAAGCAAAAAAAUGGUGAAAUAUUUUGGGCAUUCACACCUUUUAAUGUAACUUUGUAGCA ......(((((((((.((.((((((...........)))))).)).)))))))))........(((((........................))))).......(((((((...........((((((.(((((........)))))))))))((((((.((((...((.....)).........(((((............))))).)))).))))))..)))))))... (-40.76) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 313 89 45 231 183 pint:PI0092|5end_regulatory_protein_RecX_89080..89310_POSITIVE 312 230 185 221 170 pint:PI1833|5end_bacterioferritin_comigratory_protein_1773957..1774187_POSITIVE 283 90 46 80 43 pint:PI0339|5end_hypothetical_protein_315735..315965_POSITIVE 273 83 43 169 118 pint:PI0463|5end_50S_ribosomal_protein_L2_434158..434388_POSITIVE 268 68 21 178 139 pint:PI2091|5end_DNA_processing_protein_2048019..2048249_POSITIVE 268 66 21 82 40 pint:PI0592|5end_DNA_mismatch_repair_protein_540795..541025_POSITIVE 265 79 43 51 9 pint:PI1845|5end_hypothetical_protein_1791457..1791687_POSITIVE 265 89 41 91 50 pint:PI0270|5end_conserved_hypothetical_protein_261388..261618_POSITIVE 264 69 21 151 104 pint:PI2131|5end_hypothetical_protein_2080678..2080908_POSITIVE 263 88 43 60 7 pint:PI0308|5end_conserved_hypothetical_protein_290587..290817_POSITIVE 261 78 52 37 5 pint:PI2141|5end_hypothetical_protein_2087169..2087399_POSITIVE 261 78 52 215 183 pint:PI1437|5end_hypothetical_protein_1356088..1356318_POSITIVE 261 78 52 88 56 pint:PI1436|5end_hypothetical_protein_1355961..1356191_POSITIVE 261 78 52 36 4 pint:PI1064|5end_hypothetical_protein_983071..983301_POSITIVE 259 218 172 56 16 pint:PI0763|5end_thymidine_kinase_697317..697547_POSITIVE 256 212 173 173 131 pint:PI1834|5end_anaerobic_C4-dicarboxylate_membrane_transporter_1774861..1775091_POSITIVE 254 87 42 62 29 pint:PI0839|5end_conserved_hypothetical_protein_773843..774073_POSITIVE 254 82 41 204 168 pint:PI0729|5end_integrase_661428..661658_POSITIVE 253 99 61 199 160 pint:PI0418|5end_hypothetical_protein_386666..386896_POSITIVE 253 99 61 84 45 pint:PI0420|5end_hypothetical_protein_386551..386781_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 360 214 179 150 112 pint:PI1554|3end_hypothetical_protein_1470483..1470633_POSITIVE 306 69 22 150 103 pint:PI0601|3end_hypothetical_protein_549020..549170_POSITIVE 268 68 21 145 106 pint:PI2090|3end_thioesterase_family_protein_2048066..2048216_POSITIVE 265 89 41 103 62 pint:PI0269|3end_conserved_hypothetical_protein_261480..261630_POSITIVE 264 69 21 104 57 pint:PI2130|3end_DNA_polymerase_I_2080711..2080861_POSITIVE 263 88 43 60 7 pint:PI0307|3end_RNA_polymerase_sigma-70_factor,_ECF_subfamily_290667..290817_POSITIVE 254 87 42 66 33 pint:PI0838|3end_DNA_replication_and_repair_protein_773927..774077_POSITIVE 252 84 43 117 64 pint:PI0866|3end_hypothetical_protein_803993..804143_POSITIVE 248 219 177 111 61 pint:PI1700|3end_hypothetical_protein_1619243..1619393_POSITIVE 243 77 44 142 94 pint:PI1527|3end_immunoreactive_46_kDa_antigen_PG99_1449520..1449670_POSITIVE 239 73 39 59 25 pint:PI1227|3end_conserved_hypothetical_protein;_possible_DNA-binding_protein,_histone-like_family_1148974..1149124_POSITIVE 237 78 47 143 108 pint:PI1521|3end_hypothetical_protein_1441461..1441611_POSITIVE 237 78 47 52 17 pint:PI1520|3end_hypothetical_protein_1441370..1441520_POSITIVE 237 217 173 127 81 pint:PI0708|3end_conserved_hypothetical_protein_646234..646384_POSITIVE 237 94 61 151 121 pint:PI0416|3end_hypothetical_protein_386707..386857_POSITIVE 236 90 46 136 99 pint:PI1633|3end_hypothetical_protein_1552955..1553105_POSITIVE 234 59 21 63 26 pint:PI1485|3end_hypothetical_protein_1405339..1405489_POSITIVE 233 227 203 103 77 pint:PI0184|3end_possible_fibronectin_type_III_domain_protein_176516..176666_POSITIVE 232 218 172 63 23 pint:PI0792|3end_conserved_hypothetical_protein_729627..729777_POSITIVE 231 220 173 68 16 pint:PI2069|3end_ISPg3-related_transposase,_C-terminal_fragment_2029340..2029490_POSITIVE