Origin IGS: ttatattatcctccattaataaaactattatagcttttgaaattatgaaataaataactacaaattgataagattaaaatgttataaaaaattcagtctcagcaggagttattttataatttcacacctataccataatatttta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 taaaatattatggtataggtgtgaaattataaaataactcctgctgagactgaattttttataacattttaatcttatcaatttgtagttatttatttcataatttcaaaagctataatagttttattaatggaggataatataa Mask Tandem Repeat Region ================================================ ttatattatcctccattaataaaactattatagcttttgaaattatgaaataaataactacaaattgataagattaaaatgttataaaaaattcagtctcagcaggagttattttataatttcacacctataccataatatttta Find is-nt database================================================ Query_seq: FN2125:FN2126|FN2125:FN2126:DNA gyrase subunit A:DNA gyrase subunit B:<-<-:636251..636395 145 ttatattatcctccattaataaaactattatagcttttgaaattatgaaataaataactacaaattgataagattaaaatgttataaaaaattcagtctcagcaggagttattttataatttcacacctataccataatatttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN2125:FN2126|FN2125:FN2126:DNA gyrase subunit A:DNA gyrase subunit B:<-<-:636251..636395 145 ttatattatcctccattaataaaactattatagcttttgaaattatgaaataaataactacaaattgataagattaaaatgttataaaaaattcagtctcagcaggagttattttataatttcacacctataccataatatttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN2125:FN2126|FN2125:FN2126:DNA gyrase subunit A:DNA gyrase subunit B:<-<-:636251..636395 145 ttatattatcctccattaataaaactattatagcttttgaaattatgaaataaataactacaaattgataagattaaaatgttataaaaaattcagtctcagcaggagttattttataatttcacacctataccataatatttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttatattatcctccattaataaaactattatagcttttgaaattatgaaataaataactacaaattgataagattaaaatgttataaaaaattcagtctcagcaggagttattttataatttcacacctataccataatatttta Predict ORF larger than 30AA ================================================ Protein_Len: 32 Strand: + Start: 50 End: 145 ................................................. M N N Y K L I R L K C Y K K F S L S R S Y F I I S H L Y H N I L ttatattatcctccattaataaaactattatagcttttgaaattatgaaataaataactacaaattgataagattaaaatgttataaaaaattcagtctcagcaggagttattttataatttcacacctataccataatatttta 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: 81 Start: 91 End: 120 ..........................................................................................ATTCAGTCTCAGCAGGAGTTATTTTATAAT......................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ ttatattatcctccattaataaaactattatagcttttgaaattatgaaataaataactacaaattgataagattaaaatgttataaaaaattcagtctcagcaggagttattttataatttcacacctataccataatatttta Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: FN2125:FN2126|FN2125:FN2126:DNA gyrase subunit A:DNA gyrase subunit B:<-<-:636251..636395 145 ttatattatcctccattaataaaactattatagcttttgaaattatgaaataaataactacaaattgataagattaaaatgttataaaaaattcagtctcagcaggagttattttataatttcacacctataccataatatttta Intra-Species Hit: Count: 1 Min: 1 Max: 145 Len: 145 Subject: NC_003454_FN2125_FN2126|DNA gyrase subunit A:DNA gyrase subunit B|NEGATIVE:NEGATIVE|[636251,636395]|145 HSP 1 e-value: 5.0E-77 bit: 287.0 Len: 145 Query Start:1 Query End:145 Subject Strand: POSITIVE Subject Start: 1 Subject End: 145 ttatattatcctccattaataaaactattatagcttttgaaattatgaaataaataactacaaattgataagattaaaatgttataaaaaattcagtctcagcaggagttattttataatttcacacctataccataatatttta ttatattatcctccattaataaaactattatagcttttgaaattatgaaataaataactacaaattgataagattaaaatgttataaaaaattcagtctcagcaggagttattttataatttcacacctataccataatatttta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUAUAUUAUCCUCCAUUAAUAAAACUAUUAUAGCUUUUGAAAUUAUGAAAUAAAUAACUACAAAUUGAUAAGAUUAAAAUGUUAUAAAAAAUUCAGUCUCAGCAGGAGUUAUUUUAUAAUUUCACACCUAUACCAUAAUAUUUUA ...(((((........))))).......(((((....(((((((((((((((.(((((....((((.....)))).....)))))............(((.....))).)))))))))))))))...)))))............. (-18.50) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAAAUAUUAUGGUAUAGGUGUGAAAUUAUAAAAUAACUCCUGCUGAGACUGAAUUUUUUAUAACAUUUUAAUCUUAUCAAUUUGUAGUUAUUUAUUUCAUAAUUUCAAAAGCUAUAAUAGUUUUAUUAAUGGAGGAUAAUAUAA ((((((((((((((.......(((((((((.((((((...(((((((((.((((.............)))).))))).......))))....)))))).)))))))))...)))))))).))))))................... (-21.73) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 776 140 91 231 182 NC_003454:FN2125|5end_DNA_gyrase_subunit_A_636160..636390_NEGATIVE 282 140 104 182 148 NC_003454:FN0757|5end_Hypothetical_cytosolic_protein_1416201..1416431_NEGATIVE 234 140 91 189 147 NC_003454:FN1729|5end_4-amino-4-deoxychorismate_lyase_229087..229317_NEGATIVE 224 133 95 105 67 NC_003454:FN1728|5end_Pyrrolidone-carboxylate_peptidase_228366..228596_NEGATIVE 222 129 95 100 56 NC_003454:FN0807|5end_3-deoxy-manno-octulosonate_cytidylyltransferase_1467894..1468124_NEGATIVE 220 136 97 96 57 NC_003454:FN0244|5end_COP_associated_protein_868115..868345_POSITIVE 218 132 100 35 1 NC_003454:FN0748|5end_hypothetical_protein_1407543..1407773_NEGATIVE 217 138 95 53 11 NC_003454:FN0959|5end_Precorrin-2_C20-methyltransferase_1615058..1615288_NEGATIVE 200 126 89 105 62 NC_003454:FN1688|5end_Oxidoreductase_184569..184799_NEGATIVE 199 140 92 155 104 NC_003454:FN1808|5end_hypothetical_protein_289905..290135_NEGATIVE 199 48 20 176 147 NC_003454:FN1799|5end_Spermidine/putrescine_transport_system_permease_protein_potC_280776..281006_POSITIVE 195 138 101 103 62 NC_003454:FN1868|5end_Hypothetical_cytosolic_protein_360433..360663_NEGATIVE 194 129 97 108 67 NC_003454:FN1931|5end_Protease_432421..432651_NEGATIVE 192 130 92 156 117 NC_003454:FN0399|5end_Dipeptide_transport_ATP-binding_protein_dppD_1037646..1037876_POSITIVE 186 140 92 95 42 NC_003454:FN1733|5end_ATP_synthase_subunit_D_232871..233101_NEGATIVE 183 135 92 229 184 NC_003454:FN1104|5end_Holliday_junction_DNA_helicase_ruvA_1749453..1749683_POSITIVE 182 37 1 121 88 NC_003454:FN1412|5end_5-methylthioribose_kinase_2073206..2073436_NEGATIVE 182 132 100 57 19 NC_003454:FN1312|5end_Biopolymer_transport_exbB_protein_1966948..1967178_NEGATIVE 181 133 97 73 39 NC_003454:FN0113|5end_Heat-inducible_transcription_repressor_hrcA_746557..746787_POSITIVE 180 137 92 98 47 NC_003454:FN0805|5end_hypothetical_protein_1465587..1465817_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 289 117 88 79 50 NC_003454:FN0071|3end_GTP_cyclohydrolase_I_711605..711755_POSITIVE 224 133 95 133 95 NC_003454:FN1729|3end_4-amino-4-deoxychorismate_lyase_228338..228488_NEGATIVE 206 134 93 77 31 NC_003454:FN0967|3end_CbiD_protein_1619923..1620073_NEGATIVE 200 126 89 86 43 NC_003454:FN1689|3end_UDP-4-dehydro-6-deoxy-2-acetamido-D-glucose_4-reductase_184588..184738_NEGATIVE 195 138 101 83 42 NC_003454:FN1869|3end_hypothetical_protein_360453..360603_NEGATIVE 194 129 97 111 70 NC_003454:FN1932|3end_Dephospho-CoA_kinase_432418..432568_NEGATIVE 193 135 101 114 77 NC_003454:FN0589|3end_Transcriptional_regulator,_MarR_family_1242833..1242983_POSITIVE 192 140 91 137 93 NC_003454:FN0879|3end_ABC_transporter_integral_membrane_protein_1540161..1540311_NEGATIVE 192 130 92 137 98 NC_003454:FN0398|3end_Dipeptide_transport_system_permease_protein_dppC_1037707..1037857_POSITIVE 186 140 92 84 31 NC_003454:FN1734|3end_V-type_ATP_synthase_subunit_B_232882..233032_NEGATIVE 182 37 1 106 73 NC_003454:FN1413|3end_translation_initiation_factor_IF-2B_subunit_alpha_2073221..2073371_NEGATIVE 181 133 97 36 2 NC_003454:FN0112|3end_hypothetical_protein_746600..746750_POSITIVE 180 137 92 98 47 NC_003454:FN0806|3end_SpoIID_homolog_1465587..1465737_NEGATIVE 177 111 78 50 11 NC_003454:FN1827|3end_Replicative_DNA_helicase_315899..316049_NEGATIVE 177 67 30 102 61 NC_003454:FN1807|3end_hypothetical_protein_288685..288835_NEGATIVE 177 33 10 133 111 NC_003454:FN1797|3end_Spermidine/putrescine_transport_ATP-binding_protein_potA_280031..280181_POSITIVE 176 137 95 95 39 NC_003454:FN0090|3end_Ethanolamine_utilization_protein_eutQ_726844..726994_POSITIVE 175 112 77 150 119 NC_003454:FN1277|3end_Aminoacyl-histidine_dipeptidase_1935294..1935444_NEGATIVE 174 38 2 132 99 NC_003454:FN0016|3end_hypothetical_protein_654366..654516_POSITIVE 173 38 9 86 59 NC_003454:FN1921|3end_Biotin_operon_repressor_416910..417060_NEGATIVE