Origin IGS: attttcccagttgtacgctgtgaatgatgtcaccccagctattaaaaatataacagagaaaaggagaaaaaacctctttattttctcaaacataatatcacctgtcactttctttttaataatttgatttattataacatataattattaagatttggttaatttttaatagacacttattcctaatttctgatataataaatcaacttttaaaaataaggagatttataa .........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 ttataaatctccttatttttaaaagttgatttattatatcagaaattaggaataagtgtctattaaaaattaaccaaatcttaataattatatgttataataaatcaaattattaaaaagaaagtgacaggtgatattatgtttgagaaaataaagaggttttttctccttttctctgttatatttttaatagctggggtgacatcattcacagcgtacaactgggaaaat Mask Tandem Repeat Region ================================================ attttcccagttgtacgctgtgaatgatgtcaccccagctattaaaaatataacagagaaaaggagaaaaaacctctttattttctcaaacataatatcacctgtcactttctttttaataatttgatttattataacatataattattaagatttggttaatttttaatagacacttattcctaatttctgatataataaatcaacttttaaaaataaggagatttataa Find is-nt database================================================ Query_seq: FN2002:FN2003|FN2002:FN2003:Permease:bioY protein:<-->:503654..503884 231 attttcccagttgtacgctgtgaatgatgtcaccccagctattaaaaatataacagagaaaaggagaaaaaacctctttattttctcaaacataatatcacctgtcactttctttttaataatttgatttattataacatataattattaagatttggttaatttttaatagacacttattcctaatttctgatataataaatcaacttttaaaaataaggagatttataa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN2002:FN2003|FN2002:FN2003:Permease:bioY protein:<-->:503654..503884 231 attttcccagttgtacgctgtgaatgatgtcaccccagctattaaaaatataacagagaaaaggagaaaaaacctctttattttctcaaacataatatcacctgtcactttctttttaataatttgatttattataacatataattattaagatttggttaatttttaatagacacttattcctaatttctgatataataaatcaacttttaaaaataaggagatttataa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN2002:FN2003|FN2002:FN2003:Permease:bioY protein:<-->:503654..503884 231 attttcccagttgtacgctgtgaatgatgtcaccccagctattaaaaatataacagagaaaaggagaaaaaacctctttattttctcaaacataatatcacctgtcactttctttttaataatttgatttattataacatataattattaagatttggttaatttttaatagacacttattcctaatttctgatataataaatcaacttttaaaaataaggagatttataa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 attttcccagttgtacgctgtgaatgatgtcaccccagctattaaaaatataacagagaaaaggagaaaaaacctctttattttctcaaacataatatcacctgtcactttctttttaataatttgatttattataacatataattattaagatttggttaatttttaatagacacttattcctaatttctgatataataaatcaacttttaaaaataaggagatttataa Predict ORF larger than 30AA ================================================ Protein_Len: 38 Strand: + Start: 11 End: 124 .......... M Y A V N D V T P A I K N I T E K R R K N L F I F S N I I S P V T F F L I I ........................................................................................................... Protein_Len: 30 Strand: + Start: 141 End: 230 ............................................................................................................................................ M I I K I W L I F N R H L F L I S D I I N Q L L K I R R F I . Protein_Len: 45 Strand: - Start: 1 End: 135 N E W N Y A T F S T V G A I L F I V S F L L F F R K I K E F M I D G T V K K K I I Q N I M ................................................................................................ attttcccagttgtacgctgtgaatgatgtcaccccagctattaaaaatataacagagaaaaggagaaaaaacctctttattttctcaaacataatatcacctgtcactttctttttaataatttgatttattataacatataattattaagatttggttaatttttaatagacacttattcctaatttctgatataataaatcaacttttaaaaataaggagatttataa 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================================================ attttcccagttgtacgctgtgaatgatgtcaccccagctattaaaaatataacagagaaaaggagaaaaaacctctttattttctcaaacataatatcacctgtcactttctttttaataatttgatttattataacatataattattaagatttggttaatttttaatagacacttattcctaatttctgatataataaatcaacttttaaaaataaggagatttataa Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 44 HP_score: -2.5 Tail_Score: -3.41649 Start: 64 End: 87 Full_Region: ggtgatattatgttt gagaaaata aagagg ttttttctc cttttctctgttata ...............................................................gagaaaataaagaggttttttctc................................................................................................................................................ Find igs database================================================ Query_seq: FN2002:FN2003|FN2002:FN2003:Permease:bioY protein:<-->:503654..503884 231 attttcccagttgtacgctgtgaatgatgtcaccccagctattaaaaatataacagagaaaaggagaaaaaacctctttattttctcaaacataatatcacctgtcactttctttttaataatttgatttattataacatataattattaagatttggttaatttttaatagacacttattcctaatttctgatataataaatcaacttttaaaaataaggagatttataa Intra-Species Hit: Count: 1 Min: 1 Max: 231 Len: 231 Subject: NC_003454_FN2002_FN2003|Permease:bioY protein|NEGATIVE:POSITIVE|[503654,503884]|231 HSP 1 e-value: 1.0E-54 bit: 214.0 Len: 108 Query Start:1 Query End:108 Subject Strand: POSITIVE Subject Start: 1 Subject End: 108 attttcccagttgtacgctgtgaatgatgtcaccccagctattaaaaatataacagagaaaaggagaaaaaacctctttattttctcaaacataatatcacctgtcac........................................................................................................................... attttcccagttgtacgctgtgaatgatgtcaccccagctattaaaaatataacagagaaaaggagaaaaaacctctttattttctcaaacataatatcacctgtcac........................................................................................................................... HSP 2 e-value: 4.0E-26 bit: 119.0 Len: 60 Query Start:172 Query End:231 Subject Strand: POSITIVE Subject Start: 172 Subject End: 231 ...........................................................................................................................................................................gacacttattcctaatttctgatataataaatcaacttttaaaaataaggagatttataa ...........................................................................................................................................................................gacacttattcctaatttctgatataataaatcaacttttaaaaataaggagatttataa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUUUUCCCAGUUGUACGCUGUGAAUGAUGUCACCCCAGCUAUUAAAAAUAUAACAGAGAAAAGGAGAAAAAACCUCUUUAUUUUCUCAAACAUAAUAUCACCUGUCACUUUCUUUUUAAUAAUUUGAUUUAUUAUAACAUAUAAUUAUUAAGAUUUGGUUAAUUUUUAAUAGACACUUAUUCCUAAUUUCUGAUAUAAUAAAUCAACUUUUAAAAAUAAGGAGAUUUAUAA .........(((((..((((.(..((....))..)))))................(((((((((((.......))))...)))))))....))))).......(((.((((.(((((((....(((((((((((((.((...(((((.((((.....((((.....)))).....))))....)))))..)).)))))))))))))...))))))).)))).)))...... (-37.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUAUAAAUCUCCUUAUUUUUAAAAGUUGAUUUAUUAUAUCAGAAAUUAGGAAUAAGUGUCUAUUAAAAAUUAACCAAAUCUUAAUAAUUAUAUGUUAUAAUAAAUCAAAUUAUUAAAAAGAAAGUGACAGGUGAUAUUAUGUUUGAGAAAAUAAAGAGGUUUUUUCUCCUUUUCUCUGUUAUAUUUUUAAUAGCUGGGGUGACAUCAUUCACAGCGUACAACUGGGAAAAU .........((((............(((((((((((((.((.(((((((((.....((..((........))..))..)))))))..))...)).)))))))))))))..(((((((((....((((((((.((..........((((((((......))))))))......)))))))))).)))))))))(((((((((....))))).))))........)))).... (-44.39) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 856 50 1 141 92 NC_003454:FN2002|5end_Permease_503563..503793_NEGATIVE 242 109 73 100 63 NC_003454:FN1354|5end_ABC_transporter_permease_protein_2006682..2006912_NEGATIVE 226 119 75 114 66 NC_003454:FN1048|5end_Hypothetical_membrane-spanning_protein_1697911..1698141_POSITIVE 219 191 153 211 171 NC_003454:FN1727|5end_Chloride_channel_protein_227627..227857_NEGATIVE 214 40 1 187 144 NC_003454:FN0764|5end_Transporter,_LysE_family_1420327..1420557_POSITIVE 206 41 2 152 107 NC_003454:FN1501|5end_Nickel_transport_ATP-binding_protein_nikD_6710..6940_NEGATIVE 202 44 18 165 137 NC_003454:FN1599|5end_hypothetical_protein_108783..109013_NEGATIVE 194 47 3 72 22 NC_003454:FN0471|5end_Cell_surface_protein_1116525..1116755_POSITIVE 194 192 156 45 2 NC_003454:FN1586|5end_O-succinylbenzoate-CoA_synthase_98542..98772_NEGATIVE 193 148 105 100 57 NC_003454:FN1103|5end_Excinuclease_ABC_subunit_A_1746559..1746789_POSITIVE 193 215 177 111 73 NC_003454:FN0889|5end_Dihydrolipoamide_acyltransferase_1551393..1551623_NEGATIVE 193 40 13 26 2 NC_003454:FN0430|5end_50S_ribosomal_protein_L19_1071361..1071591_POSITIVE 193 125 85 112 58 NC_003454:FN0087|5end_Ethanolamine_utilization_protein_eutN_724626..724856_POSITIVE 191 41 1 175 138 NC_003454:FN0129|5end_Urease_accessory_protein_ureG_757595..757825_POSITIVE 190 143 106 227 190 NC_003454:FN1258|5end_C4-dicarboxylate-binding_protein_1914793..1915023_NEGATIVE 190 142 102 127 93 NC_003454:FN0998|5end_Dipeptide-binding_protein_1652247..1652477_POSITIVE 190 47 1 84 36 NC_003454:FN0981|5end_phosphoribosylamine--glycine_ligase_1634120..1634350_NEGATIVE 190 40 6 107 76 NC_003454:FN1994|5end_hypothetical_protein_497577..497807_POSITIVE 189 107 62 90 53 NC_003454:FN0745|5end_metal_dependent_phosphohydrolase_1403275..1403505_POSITIVE 189 118 74 97 59 NC_003454:FN0508|5end_Serine_protease_1158652..1158882_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 242 109 73 103 66 NC_003454:FN1355|3end_Integral_membrane_protein_2006679..2006829_NEGATIVE 234 86 52 83 45 NC_003454:FN1426|3end_Serine_protease_2092577..2092727_NEGATIVE 226 119 75 94 46 NC_003454:FN1047|3end_Hypothetical_membrane-spanning_protein_1697971..1698121_POSITIVE 219 191 153 116 76 NC_003454:FN1728|3end_Pyrrolidone-carboxylate_peptidase_227722..227872_NEGATIVE 202 64 25 138 99 NC_003454:FN0296|3end_Hypothetical_cytosolic_protein_929022..929172_NEGATIVE 198 60 11 85 25 NC_003454:FN1646|3end_SSU_ribosomal_protein_S10P_141449..141599_NEGATIVE 193 215 177 46 8 NC_003454:FN0890|3end_Thiamin_pyrophosphokinase_1551458..1551608_NEGATIVE 193 125 85 110 56 NC_003454:FN0086|3end_hypothetical_protein_724704..724854_POSITIVE 190 47 1 67 19 NC_003454:FN0982|3end_bifunctional_phosphoribosylaminoimidazolecarboxamide_formyltransferase/IMP_cyclohydrolase_1634137..1634287_NEGATIVE 190 40 6 100 69 NC_003454:FN1993|3end_SUA5_protein_497650..497800_POSITIVE 189 107 62 93 56 NC_003454:FN0744|3end_metal_dependent_phosphohydrolase_1403358..1403508_POSITIVE 189 118 76 46 8 NC_003454:FN1876|3end_4-methyl-5(B-hydroxyethyl)-thiazole_monophosphate_biosynthesis_enzyme_364462..364612_NEGATIVE 184 44 2 79 29 NC_003454:FN0950|3end_Precorrin-6X_reductase_1606975..1607125_NEGATIVE 184 136 92 112 71 NC_003454:FN0501|3end_Arginase_1149587..1149737_NEGATIVE 183 115 73 92 51 NC_003454:FN0135|3end_Transposase_770605..770755_POSITIVE 182 107 77 113 85 NC_003454:FN1150|3end_hypothetical_protein_1802440..1802590_NEGATIVE 182 146 103 136 98 NC_003454:FN1926|3end_Nitrogen_regulatory_IIA_protein_424352..424502_NEGATIVE 182 84 49 76 40 NC_003454:FN1879|3end_SSU_ribosomal_protein_S20P_367507..367657_POSITIVE 181 37 7 64 29 NC_003454:FN1179|3end_ATP-dependent_RNA_helicase_1839330..1839480_NEGATIVE 180 126 81 130 86 NC_003454:FN1849|3end_Coenzyme_F390_synthetase_339288..339438_POSITIVE