Origin IGS: acctgtgattactttaataaaaccattttctcgtccgtcaatcagctgcttcaaatagacgtctctgggaattgctgttctcatattttaattttctgccccatggggcacttttttcaacggcaaagatacagtatttattttaaaacaagacgtgcaatttgaaaaaagtgccacctgtggcatgtttttcaaatcaactcgttcatta .........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 taatgaacgagttgatttgaaaaacatgccacaggtggcacttttttcaaattgcacgtcttgttttaaaataaatactgtatctttgccgttgaaaaaagtgccccatggggcagaaaattaaaatatgagaacagcaattcccagagacgtctatttgaagcagctgattgacggacgagaaaatggttttattaaagtaatcacaggt Mask Tandem Repeat Region ================================================ acctgtgattactttaataaaaccattttctcgtccgtcaatcagctgcttcaaatagacgtctctgggaattgctgttctcatattttaattttctgccccatggggcacttttttcaacggcaaagatacagtatttattttaaaacaagacgtgcaatttgaaaaaagtgccacctgtggcatgtttttcaaatcaactcgttcatta Find is-nt database================================================ Query_seq: PI2079:PI2080|PI2079:PI2080:conserved hypothetical protein; possible ATPase:hypothetical protein:->->:2038022..2038232 211 acctgtgattactttaataaaaccattttctcgtccgtcaatcagctgcttcaaatagacgtctctgggaattgctgttctcatattttaattttctgccccatggggcacttttttcaacggcaaagatacagtatttattttaaaacaagacgtgcaatttgaaaaaagtgccacctgtggcatgtttttcaaatcaactcgttcatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI2079:PI2080|PI2079:PI2080:conserved hypothetical protein; possible ATPase:hypothetical protein:->->:2038022..2038232 211 acctgtgattactttaataaaaccattttctcgtccgtcaatcagctgcttcaaatagacgtctctgggaattgctgttctcatattttaattttctgccccatggggcacttttttcaacggcaaagatacagtatttattttaaaacaagacgtgcaatttgaaaaaagtgccacctgtggcatgtttttcaaatcaactcgttcatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI2079:PI2080|PI2079:PI2080:conserved hypothetical protein; possible ATPase:hypothetical protein:->->:2038022..2038232 211 acctgtgattactttaataaaaccattttctcgtccgtcaatcagctgcttcaaatagacgtctctgggaattgctgttctcatattttaattttctgccccatggggcacttttttcaacggcaaagatacagtatttattttaaaacaagacgtgcaatttgaaaaaagtgccacctgtggcatgtttttcaaatcaactcgttcatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 acctgtgattactttaataaaaccattttctcgtccgtcaatcagctgcttcaaatagacgtctctgggaattgctgttctcatattttaattttctgccccatggggcacttttttcaacggcaaagatacagtatttattttaaaacaagacgtgcaatttgaaaaaagtgccacctgtggcatgtttttcaaatcaactcgttcatta Predict ORF larger than 30AA ================================================ Protein_Len: 46 Strand: + Start: 25 End: 162 ........................ M F S S V N Q L L Q I D V S G N C C S H I L I F C P M G H F F Q R Q R Y S I Y F K T R R A I ................................................. Protein_Len: 35 Strand: - Start: 91 End: 195 .......................................................................................... N E A G H P V K K L P L S V T N I K F C S T C N S F L A V Q P M N K M ................ Protein_Len: 30 Strand: - Start: 41 End: 130 ........................................ D A A E F L R R Q S N S N E Y K L K R G W P A S K E V A F M ................................................................................. acctgtgattactttaataaaaccattttctcgtccgtcaatcagctgcttcaaatagacgtctctgggaattgctgttctcatattttaattttctgccccatggggcacttttttcaacggcaaagatacagtatttattttaaaacaagacgtgcaatttgaaaaaagtgccacctgtggcatgtttttcaaatcaactcgttcatta 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: 84 Start: 140 End: 169 ...........................................................................................................................................TTTTTCAAATTGCACGTCTTGTTTTAAAAT.......................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ acctgtgattactttaataaaaccattttctcgtccgtcaatcagctgcttcaaatagacgtctctgggaattgctgttctcatattttaattttctgccccatggggcacttttttcaacggcaaagatacagtatttattttaaaacaagacgtgcaatttgaaaaaagtgccacctgtggcatgtttttcaaatcaactcgttcatta Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 73 HP_score: -4.6 Tail_Score: -5.00616 Start: 96 End: 111 Full_Region: TCATATTTTAATTTT CTGCCC CATG GGGCAC TTTTTTCAACGGCAA ...............................................................................................CTGCCCCATGGGGCAC.................................................................................................... TransTerm Strand: + Conf: 73 HP_score: -8.1 Tail_Score: -3.60048 Start: 97 End: 110 Full_Region: CATATTTTAATTTTC TGCCC CATG GGGCA CTTTTTTCAACGGCA ................................................................................................TGCCCCATGGGGCA..................................................................................................... Find igs database================================================ Query_seq: PI2079:PI2080|PI2079:PI2080:conserved hypothetical protein; possible ATPase:hypothetical protein:->->:2038022..2038232 211 acctgtgattactttaataaaaccattttctcgtccgtcaatcagctgcttcaaatagacgtctctgggaattgctgttctcatattttaattttctgccccatggggcacttttttcaacggcaaagatacagtatttattttaaaacaagacgtgcaatttgaaaaaagtgccacctgtggcatgtttttcaaatcaactcgttcatta Intra-Species Hit: Count: 1 Min: 1 Max: 211 Len: 211 Subject: pint_PI2079_PI2080|conserved hypothetical protein; possible ATPase:hypothetical protein|POSITIVE:POSITIVE|[2038022,2038232]|211 HSP 1 e-value: 1.0E-116 bit: 418.0 Len: 211 Query Start:1 Query End:211 Subject Strand: POSITIVE Subject Start: 1 Subject End: 211 acctgtgattactttaataaaaccattttctcgtccgtcaatcagctgcttcaaatagacgtctctgggaattgctgttctcatattttaattttctgccccatggggcacttttttcaacggcaaagatacagtatttattttaaaacaagacgtgcaatttgaaaaaagtgccacctgtggcatgtttttcaaatcaactcgttcatta acctgtgattactttaataaaaccattttctcgtccgtcaatcagctgcttcaaatagacgtctctgggaattgctgttctcatattttaattttctgccccatggggcacttttttcaacggcaaagatacagtatttattttaaaacaagacgtgcaatttgaaaaaagtgccacctgtggcatgtttttcaaatcaactcgttcatta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACCUGUGAUUACUUUAAUAAAACCAUUUUCUCGUCCGUCAAUCAGCUGCUUCAAAUAGACGUCUCUGGGAAUUGCUGUUCUCAUAUUUUAAUUUUCUGCCCCAUGGGGCACUUUUUUCAACGGCAAAGAUACAGUAUUUAUUUUAAAACAAGACGUGCAAUUUGAAAAAAGUGCCACCUGUGGCAUGUUUUUCAAAUCAACUCGUUCAUUA ....((((........................(..((((.....((((.................(((((((....))))))).............(((((....)))))..........)))).((((((.......)))))).......))))..).((((((((((.((((((....)))))).))))))))))........)))).. (-46.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAUGAACGAGUUGAUUUGAAAAACAUGCCACAGGUGGCACUUUUUUCAAAUUGCACGUCUUGUUUUAAAAUAAAUACUGUAUCUUUGCCGUUGAAAAAAGUGCCCCAUGGGGCAGAAAAUUAAAAUAUGAGAACAGCAAUUCCCAGAGACGUCUAUUUGAAGCAGCUGAUUGACGGACGAGAAAAUGGUUUUAUUAAAGUAAUCACAGGU ......(((.((.(((((((((((..(((((....)))))..))))))))))))).)))(((((.(((.((((((.(((((.((((..((((..(......(((((....)))))...................((((..(((....((....))....)))...)))).)..))))..))))..)))))))))))....)))..))))). (-53.80) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 372 133 91 149 110 pint:PI0190|5end_3-dehydroquinate_dehydratase_II_180618..180848_POSITIVE 348 78 31 55 8 pint:PI0355|5end_probable__N-acetylmuramoyl-L-alanine_amidase_326157..326387_POSITIVE 305 80 35 227 171 pint:PI0624|5end_hypothetical_protein_574203..574433_POSITIVE 302 69 24 179 125 pint:PI0266|5end_DNA_primase_(bacterial_type)_257931..258161_POSITIVE 293 110 61 160 111 pint:PI1228|5end_conserved_hypothetical_protein_1149045..1149275_POSITIVE 291 70 22 152 111 pint:PI2104|5end_carboxyl-terminal_protease_2057910..2058140_POSITIVE 291 124 86 49 8 pint:PI0492|5end_hypothetical_protein_451701..451931_POSITIVE 283 68 30 142 80 pint:PI1636|5end_hypothetical_protein_1554246..1554476_POSITIVE 277 208 172 48 8 pint:PI0614|5end_glucose-6-phosphate_isomerase_563170..563400_POSITIVE 275 135 96 225 174 pint:PI1594|5end_MotA/TolQ/ExbB_proton_channel_1523528..1523758_POSITIVE 274 118 71 188 136 pint:PI1670|5end_hypothetical_protein_1583725..1583955_POSITIVE 273 124 89 211 174 pint:PI0365|5end_hypothetical_protein_335721..335951_POSITIVE 272 110 61 112 68 pint:PI0539|5end_hypothetical_protein_493406..493636_POSITIVE 271 110 64 143 95 pint:PI1643|5end_conserved_hypothetical_protein_1560936..1561166_POSITIVE 271 79 36 146 104 pint:PI0119|5end_hypothetical_protein_111506..111736_POSITIVE 270 80 36 221 169 pint:PI1580|5end_conserved_hypothetical_protein_1507833..1508063_POSITIVE 270 110 63 154 97 pint:PI0726|5end_hypothetical_protein_659042..659272_POSITIVE 269 69 23 194 150 pint:PI2131|5end_hypothetical_protein_2080678..2080908_POSITIVE 267 194 151 230 189 pint:PI0384|5end_probable_radical_SAM_domain_protein_352884..353114_POSITIVE 266 77 36 61 9 pint:PI1682|5end_aminoacyl-histidine_dipeptidase_1598303..1598533_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 348 78 31 59 12 pint:PI0354|3end_hypothetical_protein_326241..326391_POSITIVE 302 69 24 125 71 pint:PI0265|3end_conjugative_transposon_protein,_TraO_257957..258107_POSITIVE 291 70 22 96 55 pint:PI2103|3end_hypothetical_protein_2057934..2058084_POSITIVE 283 68 30 122 60 pint:PI1635|3end_hypothetical_protein_1554306..1554456_POSITIVE 269 69 23 147 103 pint:PI2130|3end_DNA_polymerase_I_2080711..2080861_POSITIVE 268 79 33 58 19 pint:PI0999|3end_hypothetical_protein_922812..922962_POSITIVE 266 82 47 89 51 pint:PI0528|3end_hypothetical_protein_483122..483272_POSITIVE 261 136 95 100 69 pint:PI1631|3end_hypothetical_protein_1552797..1552947_POSITIVE 260 140 94 59 17 pint:PI0858|3end_carbamyl_phosphate_synthase,_large_subunit_793394..793544_POSITIVE 257 80 39 120 76 pint:PI0249|3end_conserved_hypothetical_protein_247026..247176_POSITIVE 256 189 147 149 115 pint:PI1639|3end_conserved_hypothetical_protein_1558133..1558283_POSITIVE 255 110 66 98 49 pint:PI1942|3end_hypothetical_protein_1901269..1901419_POSITIVE 254 111 73 147 107 pint:PI0734|3end_ABC_transporter,_ATP-binding_/_permease_668760..668910_POSITIVE 252 82 41 129 94 pint:PI1651|3end_hypothetical_protein_1564512..1564662_POSITIVE 252 78 34 98 46 pint:PI0356|3end_hypothetical_protein_327288..327438_POSITIVE 251 110 65 97 41 pint:PI0805|3end_conserved_hypothetical_protein_743807..743957_POSITIVE 249 69 23 120 54 pint:PI0683|3end_hypothetical_protein_619797..619947_POSITIVE 248 81 41 46 7 pint:PI0935|3end_collagenase,_protease_868320..868470_POSITIVE 248 135 95 121 69 pint:PI0427|3end_conserved_hypothetical_protein_393088..393238_POSITIVE 247 191 161 54 18 pint:PI1399|3end_hypothetical_protein_1320844..1320994_POSITIVE