Origin IGS: cggttgttcaaaaccgagctcttcaatagcgcggcgaatctcttcgctaacgcctaattcttcaaatgttttcaaactgtttcttttttatgaaagtctgaacagaccatacaattaaagacactgccatttaaacacaccgtagcgatgtgtttcaacctaaatgtcagaaactttaaatgctataacccactcaaacttttgtctattattactcgttcacccaatcggttgtcagccagccataatagacaacactctgt .........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 acagagtgttgtctattatggctggctgacaaccgattgggtgaacgagtaataatagacaaaagtttgagtgggttatagcatttaaagtttctgacatttaggttgaaacacatcgctacggtgtgtttaaatggcagtgtctttaattgtatggtctgttcagactttcataaaaaagaaacagtttgaaaacatttgaagaattaggcgttagcgaagagattcgccgcgctattgaagagctcggttttgaacaaccg Mask Tandem Repeat Region ================================================ cggttgttcaaaaccgagctcttcaatagcgcggcgaatctcttcgctaacgcctaattcttcaaatgttttcaaactgtttcttttttatgaaagtctgaacagaccatacaattaaagacactgccatttaaacacaccgtagcgatgtgtttcaacctaaatgtcagaaactttaaatgctataacccactcaaacttttgtctattattactcgttcacccaatcggttgtcagccagccataatagacaacactctgt Find is-nt database================================================ Query_seq: PI0760:PI0761|PI0760:PI0761:ATP-dependent RNA helicase, DEAD/DEAH box family:hypothetical protein:->->:696050..696312 263 cggttgttcaaaaccgagctcttcaatagcgcggcgaatctcttcgctaacgcctaattcttcaaatgttttcaaactgtttcttttttatgaaagtctgaacagaccatacaattaaagacactgccatttaaacacaccgtagcgatgtgtttcaacctaaatgtcagaaactttaaatgctataacccactcaaacttttgtctattattactcgttcacccaatcggttgtcagccagccataatagacaacactctgt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI0760:PI0761|PI0760:PI0761:ATP-dependent RNA helicase, DEAD/DEAH box family:hypothetical protein:->->:696050..696312 263 cggttgttcaaaaccgagctcttcaatagcgcggcgaatctcttcgctaacgcctaattcttcaaatgttttcaaactgtttcttttttatgaaagtctgaacagaccatacaattaaagacactgccatttaaacacaccgtagcgatgtgtttcaacctaaatgtcagaaactttaaatgctataacccactcaaacttttgtctattattactcgttcacccaatcggttgtcagccagccataatagacaacactctgt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI0760:PI0761|PI0760:PI0761:ATP-dependent RNA helicase, DEAD/DEAH box family:hypothetical protein:->->:696050..696312 263 cggttgttcaaaaccgagctcttcaatagcgcggcgaatctcttcgctaacgcctaattcttcaaatgttttcaaactgtttcttttttatgaaagtctgaacagaccatacaattaaagacactgccatttaaacacaccgtagcgatgtgtttcaacctaaatgtcagaaactttaaatgctataacccactcaaacttttgtctattattactcgttcacccaatcggttgtcagccagccataatagacaacactctgt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 cggttgttcaaaaccgagctcttcaatagcgcggcgaatctcttcgctaacgcctaattcttcaaatgttttcaaactgtttcttttttatgaaagtctgaacagaccatacaattaaagacactgccatttaaacacaccgtagcgatgtgtttcaacctaaatgtcagaaactttaaatgctataacccactcaaacttttgtctattattactcgttcacccaatcggttgtcagccagccataatagacaacactctgt Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: + Start: 26 End: 115 ......................... M A R R I S S L T P N S S N V F K L F L F Y E S L N R P Y N .................................................................................................................................................... Protein_Len: 51 Strand: + Start: 109 End: 261 ............................................................................................................ M Q L K T L P F K H T V A M C F N L N V R N F K C Y N P L K L L S I I T R S P N R L S A S H N R Q H S .. Protein_Len: 33 Strand: + Start: 164 End: 262 ................................................................................................................................................................... M S E T L N A I T H S N F C L L L L V H P I G C Q P A I I D N T L . Protein_Len: 32 Strand: - Start: 75 End: 170 .......................................................................... V T E K K H F D S C V M C N F V S G N L C V T A I H K L R F T M ............................................................................................. cggttgttcaaaaccgagctcttcaatagcgcggcgaatctcttcgctaacgcctaattcttcaaatgttttcaaactgtttcttttttatgaaagtctgaacagaccatacaattaaagacactgccatttaaacacaccgtagcgatgtgtttcaacctaaatgtcagaaactttaaatgctataacccactcaaacttttgtctattattactcgttcacccaatcggttgtcagccagccataatagacaacactctgt 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================================================ cggttgttcaaaaccgagctcttcaatagcgcggcgaatctcttcgctaacgcctaattcttcaaatgttttcaaactgtttcttttttatgaaagtctgaacagaccatacaattaaagacactgccatttaaacacaccgtagcgatgtgtttcaacctaaatgtcagaaactttaaatgctataacccactcaaacttttgtctattattactcgttcacccaatcggttgtcagccagccataatagacaacactctgt Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 74 HP_score: -8.7 Tail_Score: -3.65529 Start: 136 End: 152 Full_Region: acatttaggttgaaa cacatcg cta cggtgtg tttaaatggcagtgt .......................................................................................................................................cacatcgctacggtgtg............................................................................................................... Find igs database================================================ Query_seq: PI0760:PI0761|PI0760:PI0761:ATP-dependent RNA helicase, DEAD/DEAH box family:hypothetical protein:->->:696050..696312 263 cggttgttcaaaaccgagctcttcaatagcgcggcgaatctcttcgctaacgcctaattcttcaaatgttttcaaactgtttcttttttatgaaagtctgaacagaccatacaattaaagacactgccatttaaacacaccgtagcgatgtgtttcaacctaaatgtcagaaactttaaatgctataacccactcaaacttttgtctattattactcgttcacccaatcggttgtcagccagccataatagacaacactctgt Intra-Species Hit: Count: 1 Min: 1 Max: 263 Len: 263 Subject: pint_PI0760_PI0761|ATP-dependent RNA helicase, DEAD/DEAH box family:hypothetical protein|POSITIVE:POSITIVE|[696050,696312]|263 HSP 1 e-value: 1.0E-147 bit: 521.0 Len: 263 Query Start:1 Query End:263 Subject Strand: POSITIVE Subject Start: 1 Subject End: 263 cggttgttcaaaaccgagctcttcaatagcgcggcgaatctcttcgctaacgcctaattcttcaaatgttttcaaactgtttcttttttatgaaagtctgaacagaccatacaattaaagacactgccatttaaacacaccgtagcgatgtgtttcaacctaaatgtcagaaactttaaatgctataacccactcaaacttttgtctattattactcgttcacccaatcggttgtcagccagccataatagacaacactctgt cggttgttcaaaaccgagctcttcaatagcgcggcgaatctcttcgctaacgcctaattcttcaaatgttttcaaactgtttcttttttatgaaagtctgaacagaccatacaattaaagacactgccatttaaacacaccgtagcgatgtgtttcaacctaaatgtcagaaactttaaatgctataacccactcaaacttttgtctattattactcgttcacccaatcggttgtcagccagccataatagacaacactctgt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CGGUUGUUCAAAACCGAGCUCUUCAAUAGCGCGGCGAAUCUCUUCGCUAACGCCUAAUUCUUCAAAUGUUUUCAAACUGUUUCUUUUUUAUGAAAGUCUGAACAGACCAUACAAUUAAAGACACUGCCAUUUAAACACACCGUAGCGAUGUGUUUCAACCUAAAUGUCAGAAACUUUAAAUGCUAUAACCCACUCAAACUUUUGUCUAUUAUUACUCGUUCACCCAAUCGGUUGUCAGCCAGCCAUAAUAGACAACACUCUGU (((((......))))).........(((((..((((((....))))))............................(((((((((((....)))))...)))))).........((((((...(((.((((((((((((.((...)).))))))......)))))).)))...))))))..)))))...............(((((((((((..((.(((((.((....)).))..))).))..)))))))))))........ (-53.50) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACAGAGUGUUGUCUAUUAUGGCUGGCUGACAACCGAUUGGGUGAACGAGUAAUAAUAGACAAAAGUUUGAGUGGGUUAUAGCAUUUAAAGUUUCUGACAUUUAGGUUGAAACACAUCGCUACGGUGUGUUUAAAUGGCAGUGUCUUUAAUUGUAUGGUCUGUUCAGACUUUCAUAAAAAAGAAACAGUUUGAAAACAUUUGAAGAAUUAGGCGUUAGCGAAGAGAUUCGCCGCGCUAUUGAAGAGCUCGGUUUUGAACAACCG .((((.(((((((((((((.(((.(......(((.....)))...).))).))))))))).((((((((((..(..((((.((.((((((...(((.((((((......(((((((((...))))))))))))))).)))...)))))).))))))..)..))))))))))...........)))).))))..................(((((..(((((....))))).)))))...........(((((......))))) (-78.10) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 372 54 15 58 25 pint:PI1634|5end_conserved_hypothetical_protein_1553179..1553409_POSITIVE 372 54 15 58 25 pint:PI0340|5end_conserved_hypothetical_protein_316095..316325_POSITIVE 344 49 16 45 5 pint:PI1086|5end_pyruvate:ferredoxin_oxidoreductase_1006602..1006832_POSITIVE 337 52 13 71 29 pint:PI2052|5end_hypothetical_protein_2008594..2008824_POSITIVE 322 246 201 169 117 pint:PI0676|5end_hypothetical_protein_614576..614806_POSITIVE 307 55 14 192 151 pint:PI0257|5end_conjugative_transposon_protein,_TraF_249348..249578_POSITIVE 298 70 21 228 181 pint:PI1580|5end_conserved_hypothetical_protein_1507833..1508063_POSITIVE 297 58 13 88 26 pint:PI1438|5end_penicillin_tolerance_protein/steroid_biosynthesis_1356263..1356493_POSITIVE 294 54 13 144 112 pint:PI1575|5end_LemA_protein_1501143..1501373_POSITIVE 293 250 201 155 92 pint:PI2044|5end_hypothetical_protein_1996999..1997229_POSITIVE 292 47 1 172 128 pint:PI1757|5end_hypothetical_protein_1683934..1684164_POSITIVE 290 49 15 114 76 pint:PI2104|5end_carboxyl-terminal_protease_2057910..2058140_POSITIVE 290 246 201 124 75 pint:PI0989|5end_mannose-1-phosphate_guanylyltransferase_912833..913063_POSITIVE 290 60 13 181 123 pint:PI0869|5end_possible_exodeoxyribonuclease_VII_(small_subunit)_805518..805748_POSITIVE 290 60 15 230 194 pint:PI0635|5end_dephospho-CoA_kinase_580954..581184_POSITIVE 289 56 13 199 135 pint:PI2126|5end_conserved_hypothetical_protein_2074907..2075137_POSITIVE 287 143 102 184 144 pint:PI1036|5end_ATP-dependent__Lon_protease_954446..954676_POSITIVE 287 48 1 67 15 pint:PI0529|5end_hypothetical_protein_483026..483256_POSITIVE 284 53 14 99 60 pint:PI0608|5end_isochorismate_synthase_555487..555717_POSITIVE 282 47 1 208 157 pint:PI0263|5end_conjugative_transposon_protein,_TraM_255256..255486_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 367 55 16 119 79 pint:PI1715|3end_conserved_hypothetical_protein;_possible_DNA-binding_protein,_histone-like_family_1632324..1632474_POSITIVE 338 56 12 48 5 pint:PI0683|3end_hypothetical_protein_619797..619947_POSITIVE 305 47 1 132 96 pint:PI1651|3end_hypothetical_protein_1564512..1564662_POSITIVE 294 54 13 147 115 pint:PI1574|3end_conserved_hypothetical_protein_1501226..1501376_POSITIVE 290 49 15 58 20 pint:PI2103|3end_hypothetical_protein_2057934..2058084_POSITIVE 287 48 1 83 31 pint:PI0528|3end_hypothetical_protein_483122..483272_POSITIVE 284 57 13 151 90 pint:PI1437|3end_hypothetical_protein_1356407..1356557_POSITIVE 284 53 15 56 20 pint:PI0951|3end_hypothetical_protein_885448..885598_POSITIVE 284 53 14 80 41 pint:PI0607|3end_2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxy_lic_acid_synthase/2-oxoglutarate_decarboxylase_555548..555698_POSITIVE 278 246 201 88 41 pint:PI0359|3end_hypothetical_protein_328835..328985_POSITIVE 276 54 31 21 2 pint:PI1632|3end_hypothetical_protein_1553222..1553372_POSITIVE 276 54 31 21 2 pint:PI0339|3end_hypothetical_protein_316138..316288_POSITIVE 276 48 1 125 68 pint:PI0117|3end_ribonuclease_HI_111314..111464_POSITIVE 274 55 13 64 26 pint:PI0838|3end_DNA_replication_and_repair_protein_773927..774077_POSITIVE 272 59 15 132 80 pint:PI0944|3end_hypothetical_protein_875249..875399_POSITIVE 270 48 1 100 35 pint:PI0728|3end_integrase_661508..661658_POSITIVE 268 54 14 43 2 pint:PI0249|3end_conserved_hypothetical_protein_247026..247176_POSITIVE 267 48 1 68 21 pint:PI0584|3end_hypothetical_protein_527656..527806_POSITIVE 266 63 29 137 99 pint:PI2155|3end_hypothetical_protein_2101052..2101202_POSITIVE 266 53 13 89 32 pint:PI0348|3end_conserved_hypothetical_protein_323211..323361_POSITIVE