Origin IGS: aattgctttcaatggttcgctgtcgccagcaaaagcagccgatgttcctattaacatcatcactgccatgattaattttttcatattagtttataatttaaagattaatactcgttattaagctctctctattcaatatatacgattttccaataacgtttaaacttatcactttatttta .........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 taaaataaagtgataagtttaaacgttattggaaaatcgtatatattgaatagagagagcttaataacgagtattaatctttaaattataaactaatatgaaaaaattaatcatggcagtgatgatgttaataggaacatcggctgcttttgctggcgacagcgaaccattgaaagcaatt Mask Tandem Repeat Region ================================================ aattgctttcaatggttcgctgtcgccagcaaaagcagccgatgttcctattaacatcatcactgccatgattaattttttcatattagtttataatttaaagattaatactcgttattaagctctctctattcaatatatacgattttccaataacgtttaaacttatcactttatttta Find is-nt database================================================ Query_seq: PI0779:PI0780|PI0779:PI0780:predicted TPR-repeat-containing protein:DNA gyrase, subunit A (DNA topoisomerase (ATP-hydrolyzing)):->->:715861..716041 181 aattgctttcaatggttcgctgtcgccagcaaaagcagccgatgttcctattaacatcatcactgccatgattaattttttcatattagtttataatttaaagattaatactcgttattaagctctctctattcaatatatacgattttccaataacgtttaaacttatcactttatttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI0779:PI0780|PI0779:PI0780:predicted TPR-repeat-containing protein:DNA gyrase, subunit A (DNA topoisomerase (ATP-hydrolyzing)):->->:715861..716041 181 aattgctttcaatggttcgctgtcgccagcaaaagcagccgatgttcctattaacatcatcactgccatgattaattttttcatattagtttataatttaaagattaatactcgttattaagctctctctattcaatatatacgattttccaataacgtttaaacttatcactttatttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI0779:PI0780|PI0779:PI0780:predicted TPR-repeat-containing protein:DNA gyrase, subunit A (DNA topoisomerase (ATP-hydrolyzing)):->->:715861..716041 181 aattgctttcaatggttcgctgtcgccagcaaaagcagccgatgttcctattaacatcatcactgccatgattaattttttcatattagtttataatttaaagattaatactcgttattaagctctctctattcaatatatacgattttccaataacgtttaaacttatcactttatttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aattgctttcaatggttcgctgtcgccagcaaaagcagccgatgttcctattaacatcatcactgccatgattaattttttcatattagtttataatttaaagattaatactcgttattaagctctctctattcaatatatacgattttccaataacgtttaaacttatcactttatttta Predict ORF larger than 30AA ================================================ Protein_Len: 39 Strand: + Start: 2 End: 118 . M A F N G S L S P A K A A D V P I N I I T A M I N F F I L V Y N L K I N T R Y ............................................................... aattgctttcaatggttcgctgtcgccagcaaaagcagccgatgttcctattaacatcatcactgccatgattaattttttcatattagtttataatttaaagattaatactcgttattaagctctctctattcaatatatacgattttccaataacgtttaaacttatcactttatttta 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================================================ aattgctttcaatggttcgctgtcgccagcaaaagcagccgatgttcctattaacatcatcactgccatgattaattttttcatattagtttataatttaaagattaatactcgttattaagctctctctattcaatatatacgattttccaataacgtttaaacttatcactttatttta Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 45 HP_score: -2.4 Tail_Score: -3.48766 Start: 105 End: 121 Full_Region: ttgaatagagagagc ttaata acgag tattaa tctttaaattataaa ........................................................................................................ttaataacgagtattaa............................................................ Find igs database================================================ Query_seq: PI0779:PI0780|PI0779:PI0780:predicted TPR-repeat-containing protein:DNA gyrase, subunit A (DNA topoisomerase (ATP-hydrolyzing)):->->:715861..716041 181 aattgctttcaatggttcgctgtcgccagcaaaagcagccgatgttcctattaacatcatcactgccatgattaattttttcatattagtttataatttaaagattaatactcgttattaagctctctctattcaatatatacgattttccaataacgtttaaacttatcactttatttta Intra-Species Hit: Count: 1 Min: 1 Max: 181 Len: 181 Subject: pint_PI0779_PI0780|predicted TPR-repeat-containing protein:DNA gyrase, subunit A (DNA topoisomerase (ATP-hydrolyzing))|POSITIVE:POSITIVE|[715861,716041]|181 HSP 1 e-value: 2.0E-98 bit: 359.0 Len: 181 Query Start:1 Query End:181 Subject Strand: POSITIVE Subject Start: 1 Subject End: 181 aattgctttcaatggttcgctgtcgccagcaaaagcagccgatgttcctattaacatcatcactgccatgattaattttttcatattagtttataatttaaagattaatactcgttattaagctctctctattcaatatatacgattttccaataacgtttaaacttatcactttatttta aattgctttcaatggttcgctgtcgccagcaaaagcagccgatgttcctattaacatcatcactgccatgattaattttttcatattagtttataatttaaagattaatactcgttattaagctctctctattcaatatatacgattttccaataacgtttaaacttatcactttatttta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUUGCUUUCAAUGGUUCGCUGUCGCCAGCAAAAGCAGCCGAUGUUCCUAUUAACAUCAUCACUGCCAUGAUUAAUUUUUUCAUAUUAGUUUAUAAUUUAAAGAUUAAUACUCGUUAUUAAGCUCUCUCUAUUCAAUAUAUACGAUUUUCCAAUAACGUUUAAACUUAUCACUUUAUUUUA ....((((..(((((...((((....))))....((((..((((((......))))))....))))....((((((((((....((((.....))))..))))))))))..)))))...)))).......................................................... (-24.30) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAAAUAAAGUGAUAAGUUUAAACGUUAUUGGAAAAUCGUAUAUAUUGAAUAGAGAGAGCUUAAUAACGAGUAUUAAUCUUUAAAUUAUAAACUAAUAUGAAAAAAUUAAUCAUGGCAGUGAUGAUGUUAAUAGGAACAUCGGCUGCUUUUGCUGGCGACAGCGAACCAUUGAAAGCAAUU .........(((((.(((((...(((((((((....((...(((.....)))..))....)))))))))................(((((......)))))..))))).))))).(((((..(((((((......)))))))))))).(((((((....)))))))............... (-36.20) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 333 44 3 157 107 pint:PI1157|5end_hypothetical_protein_1081704..1081934_POSITIVE 332 50 11 229 188 pint:PI0883|5end_para-aminobenzoate_synthase_component_I_816131..816361_POSITIVE 322 42 3 42 6 pint:PI1811|5end_conserved_hypothetical_protein_1749518..1749748_POSITIVE 322 67 25 223 167 pint:PI0040|5end_conserved_hypothetical_protein_(possible_integral_membrane_protein)_41010..41240_POSITIVE 321 60 14 71 22 pint:PI0810|5end_hypothetical_protein_746743..746973_POSITIVE 321 60 14 66 17 pint:PI0811|5end_protease/hemagglutinin_PrtT,_streptopain_family_746738..746968_POSITIVE 315 49 13 138 92 pint:PI1618|5end_hypothetical_protein_1542670..1542900_POSITIVE 311 46 6 209 170 pint:PI0701|5end_hypothetical_protein_638356..638586_POSITIVE 308 45 4 210 165 pint:PI0877|5end_hypothetical_protein_811378..811608_POSITIVE 307 48 4 231 187 pint:PI0334|5end_hypothetical_protein_313234..313464_POSITIVE 303 68 22 148 94 pint:PI1475|5end_possible_short_chain_dehydrogenase_1397142..1397372_POSITIVE 299 42 10 165 127 pint:PI0926|5end_hypothetical_protein_856824..857054_POSITIVE 297 49 4 134 92 pint:PI0009|5end_NAD-dependent_epimerase/dehydratase_family_protein_9653..9883_POSITIVE 295 59 12 201 157 pint:PI0981|5end_outer_membrane_protein,_TonB_dependent_receptor_906968..907198_POSITIVE 294 47 4 109 62 pint:PI0688|5end_hypothetical_protein_625458..625688_POSITIVE 292 48 2 213 146 pint:PI0854|5end_MiaB-like_tRNA_modifying_enzyme_786513..786743_POSITIVE 290 59 17 66 34 pint:PI0356|5end_hypothetical_protein_326642..326872_POSITIVE 289 49 5 229 177 pint:PI1636|5end_hypothetical_protein_1554246..1554476_POSITIVE 288 50 4 71 19 pint:PI1068|5end_nucleolar_protein,_Sun_(Fmu)_family_protein;_tRNA/rRNA_cytosine-C5-methylase_984743..984973_POSITIVE 285 47 5 64 10 pint:PI0341|5end_conserved_hypothetical_protein_317038..317268_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 364 60 12 75 24 pint:PI0027|3end_aminopeptidase_C_31756..31906_POSITIVE 357 44 11 93 54 pint:PI1722|3end_possible_peptidyl-prolyl_cis-trans_isomerase_1640995..1641145_POSITIVE 345 70 25 120 74 pint:PI0810|3end_hypothetical_protein_747026..747176_POSITIVE 324 40 3 132 101 pint:PI1227|3end_conserved_hypothetical_protein;_possible_DNA-binding_protein,_histone-like_family_1148974..1149124_POSITIVE 315 49 13 57 11 pint:PI1616|3end_hypothetical_protein_1542669..1542819_POSITIVE 312 48 1 137 91 pint:PI1554|3end_hypothetical_protein_1470483..1470633_POSITIVE 310 48 19 125 87 pint:PI0421|3end_hypothetical_protein_387774..387924_POSITIVE 308 44 12 93 52 pint:PI1716|3end_hypothetical_protein_1632006..1632156_POSITIVE 305 46 5 62 11 pint:PI1815|3end_polyphosphate-selective_porin_O_1754510..1754660_POSITIVE 298 48 8 80 32 pint:PI0365|3end_hypothetical_protein_336118..336268_POSITIVE 292 48 5 145 98 pint:PI0330|3end_hypothetical_protein_312545..312695_POSITIVE 291 42 6 141 94 pint:PI0160|3end_conserved_hypothetical_protein_153268..153418_POSITIVE 290 39 3 149 104 pint:PI1156|3end_possible_glycerate_kinase_family_protein_1081781..1081931_POSITIVE 290 59 17 42 10 pint:PI0355|3end_probable__N-acetylmuramoyl-L-alanine_amidase_326698..326848_POSITIVE 288 49 1 58 18 pint:PI1608|3end_possible_Na+/H+_anti-porter_1536300..1536450_POSITIVE 288 50 4 59 7 pint:PI1067|3end_thymidylate_synthase_984811..984961_POSITIVE 282 36 12 139 112 pint:PI1240|3end_probable_Xaa-Pro_dipeptidase_(aminopeptidase_P)_1166272..1166422_POSITIVE 281 48 2 148 106 pint:PI0943|3end_conserved_hypothetical_protein_875991..876141_POSITIVE 281 44 5 144 104 pint:PI0126|3end_conserved_hypothetical_protein_118589..118739_POSITIVE 280 70 24 121 69 pint:PI0704|3end_conserved_hypothetical_protein_641364..641514_POSITIVE