Origin IGS: aattataatgctaataaaacttatatgtttactaataaagtttttcatatttcctcttttctaaaataaaaaactttcttaggattgctccaaagaaagttattattaagatggtactcccttcgttggcattatccaaatcaggtactatgggtctaagaaaaaaggttctaatctcagcacaaagctccccagtacatatattattgtattttacttttctattttaaaattttttattctatttgtcaac .........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 gttgacaaatagaataaaaaattttaaaatagaaaagtaaaatacaataatatatgtactggggagctttgtgctgagattagaaccttttttcttagacccatagtacctgatttggataatgccaacgaagggagtaccatcttaataataactttctttggagcaatcctaagaaagttttttattttagaaaagaggaaatatgaaaaactttattagtaaacatataagttttattagcattataatt Mask Tandem Repeat Region ================================================ aattataatgctaataaaacttatatgtttactaataaagtttttcatatttcctcttttctaaaataaaaaactttcttaggattgctccaaagaaagttattattaagatggtactcccttcgttggcattatccaaatcaggtactatgggtctaagaaaaaaggttctaatctcagcacaaagctccccagtacatatattattgtattttacttttctattttaaaattttttattctatttgtcaac Find is-nt database================================================ Query_seq: FN0237:FN0238|FN0237:FN0238:ABC transporter permease protein:hypothetical protein:<-<-:862219..862471 253 aattataatgctaataaaacttatatgtttactaataaagtttttcatatttcctcttttctaaaataaaaaactttcttaggattgctccaaagaaagttattattaagatggtactcccttcgttggcattatccaaatcaggtactatgggtctaagaaaaaaggttctaatctcagcacaaagctccccagtacatatattattgtattttacttttctattttaaaattttttattctatttgtcaac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN0237:FN0238|FN0237:FN0238:ABC transporter permease protein:hypothetical protein:<-<-:862219..862471 253 aattataatgctaataaaacttatatgtttactaataaagtttttcatatttcctcttttctaaaataaaaaactttcttaggattgctccaaagaaagttattattaagatggtactcccttcgttggcattatccaaatcaggtactatgggtctaagaaaaaaggttctaatctcagcacaaagctccccagtacatatattattgtattttacttttctattttaaaattttttattctatttgtcaac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN0237:FN0238|FN0237:FN0238:ABC transporter permease protein:hypothetical protein:<-<-:862219..862471 253 aattataatgctaataaaacttatatgtttactaataaagtttttcatatttcctcttttctaaaataaaaaactttcttaggattgctccaaagaaagttattattaagatggtactcccttcgttggcattatccaaatcaggtactatgggtctaagaaaaaaggttctaatctcagcacaaagctccccagtacatatattattgtattttacttttctattttaaaattttttattctatttgtcaac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aattataatgctaataaaacttatatgtttactaataaagtttttcatatttcctcttttctaaaataaaaaactttcttaggattgctccaaagaaagttattattaagatggtactcccttcgttggcattatccaaatcaggtactatgggtctaagaaaaaaggttctaatctcagcacaaagctccccagtacatatattattgtattttacttttctattttaaaattttttattctatttgtcaac Predict ORF larger than 30AA ================================================ Protein_Len: 54 Strand: + Start: 66 End: 227 ................................................................. M K N F L R I A P K K V I I K M V L P S L A L S K S G T M G L R K K V L I S A Q S S P V H I L L Y F T F L F .......................... Protein_Len: 41 Strand: + Start: 131 End: 253 .................................................................................................................................. M I Q I R Y Y G S K K K G S N L S T K L P S T Y I I V F Y F S I L K F F I L F V N Protein_Len: 56 Strand: - Start: 35 End: 202 .................................. Y L K E Y K R K E L I F F K R L I A G F F T I I L I T S G E N A N D L D P V I P R L F F T R I E A C L E G T C M ................................................... aattataatgctaataaaacttatatgtttactaataaagtttttcatatttcctcttttctaaaataaaaaactttcttaggattgctccaaagaaagttattattaagatggtactcccttcgttggcattatccaaatcaggtactatgggtctaagaaaaaaggttctaatctcagcacaaagctccccagtacatatattattgtattttacttttctattttaaaattttttattctatttgtcaac 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: 91 Start: 224 End: 253 ...............................................................................................................................................................................................................................GTTGACAAATAGAATAAAAAATTTTAAAAT Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aattataatgctaataaaacttatatgtttactaataaagtttttcatatttcctcttttctaaaataaaaaactttcttaggattgctccaaagaaagttattattaagatggtactcccttcgttggcattatccaaatcaggtactatgggtctaagaaaaaaggttctaatctcagcacaaagctccccagtacatatattattgtattttacttttctattttaaaattttttattctatttgtcaac Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 100 HP_score: -9.1 Tail_Score: -5.79595 Start: 74 End: 99 Full_Region: ccatcttaataataa ctttctttgga gcaa tcctaagaaag ttttttattttagaa .........................................................................ctttctttggagcaatcctaagaaag.......................................................................................................................................................... Find igs database================================================ Query_seq: FN0237:FN0238|FN0237:FN0238:ABC transporter permease protein:hypothetical protein:<-<-:862219..862471 253 aattataatgctaataaaacttatatgtttactaataaagtttttcatatttcctcttttctaaaataaaaaactttcttaggattgctccaaagaaagttattattaagatggtactcccttcgttggcattatccaaatcaggtactatgggtctaagaaaaaaggttctaatctcagcacaaagctccccagtacatatattattgtattttacttttctattttaaaattttttattctatttgtcaac Intra-Species Hit: Count: 1 Min: 1 Max: 199 Len: 199 Subject: NC_003454_FN0237_FN0238|ABC transporter permease protein:hypothetical protein|NEGATIVE:NEGATIVE|[862219,862471]|253 HSP 1 e-value: 1.0E-109 bit: 394.0 Len: 199 Query Start:1 Query End:199 Subject Strand: POSITIVE Subject Start: 1 Subject End: 199 aattataatgctaataaaacttatatgtttactaataaagtttttcatatttcctcttttctaaaataaaaaactttcttaggattgctccaaagaaagttattattaagatggtactcccttcgttggcattatccaaatcaggtactatgggtctaagaaaaaaggttctaatctcagcacaaagctccccagtaca...................................................... aattataatgctaataaaacttatatgtttactaataaagtttttcatatttcctcttttctaaaataaaaaactttcttaggattgctccaaagaaagttattattaagatggtactcccttcgttggcattatccaaatcaggtactatgggtctaagaaaaaaggttctaatctcagcacaaagctccccagtaca...................................................... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUUAUAAUGCUAAUAAAACUUAUAUGUUUACUAAUAAAGUUUUUCAUAUUUCCUCUUUUCUAAAAUAAAAAACUUUCUUAGGAUUGCUCCAAAGAAAGUUAUUAUUAAGAUGGUACUCCCUUCGUUGGCAUUAUCCAAAUCAGGUACUAUGGGUCUAAGAAAAAAGGUUCUAAUCUCAGCACAAAGCUCCCCAGUACA ....(((((((((((.......(((((...(((.....)))....)))))..((((((......(((((..(((((((((.(((....))).))))))))).))))))))).))..........))))))))))).........(((((..(((....((((......))))......(((.....))).)))))))). (-39.00) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGUACUGGGGAGCUUUGUGCUGAGAUUAGAACCUUUUUUCUUAGACCCAUAGUACCUGAUUUGGAUAAUGCCAACGAAGGGAGUACCAUCUUAAUAAUAACUUUCUUUGGAGCAAUCCUAAGAAAGUUUUUUAUUUUAGAAAAGAGGAAAUAUGAAAAACUUUAUUAGUAAACAUAUAAGUUUUAUUAGCAUUAUAAUU ................(((((((........((((((((((.............(((...((((......))))...)))............(((((.(((((((((.(((....))).)))))))))..)))))..))))))))))..(((((....(((.....)))...)))))........)))))))....... (-43.00) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 874 130 81 221 172 NC_003454:FN0237|5end_ABC_transporter_permease_protein_862128..862358_NEGATIVE 471 160 115 177 134 NC_003454:FN1759|5end_Hydroxymethylpyrimidine_kinase_254765..254995_NEGATIVE 265 64 23 113 61 NC_003454:FN1968|5end_Hemin_transport_system_ATP-binding_protein_hmuV_467189..467419_NEGATIVE 241 70 32 92 49 NC_003454:FN1321|5end_Acetoacetate_metabolism_regulatory_protein_atoC_1977390..1977620_NEGATIVE 241 129 81 188 141 NC_003454:FN1594|5end_Nitrogen_fixation_protein_RNFG_104893..105123_NEGATIVE 240 150 109 192 158 NC_003454:FN1124|5end_Outer_membrane_porin_F_1769005..1769235_NEGATIVE 236 80 36 208 152 NC_003454:FN1582|5end_hypothetical_protein_94957..95187_NEGATIVE 230 147 117 139 98 NC_003454:FN1897|5end_ABC_transporter_integral_membrane_protein_384984..385214_NEGATIVE 227 62 25 115 67 NC_003454:FN1974|5end_DNA/RNA_helicase_(DEAD/DEAH_BOX_family)_475526..475756_NEGATIVE 222 61 22 225 193 NC_003454:FN1818|5end_Hemolysin_activator_protein_precursor_306955..307185_NEGATIVE 219 180 136 60 22 NC_003454:FN0813|5end_Transcriptional_regulator,_TetR_family_1472622..1472852_NEGATIVE 216 110 74 139 101 NC_003454:FN1314|5end_hypothetical_protein_1968682..1968912_NEGATIVE 216 63 21 105 63 NC_003454:FN0240|5end_Thymidylate_synthase_863894..864124_POSITIVE 214 190 142 227 176 NC_003454:FN0425|5end_Hypothetical_cytosolic_protein_1068030..1068260_POSITIVE 210 63 21 60 18 NC_003454:FN0951|5end_Precorrin-3B_C17-methyltransferase_1608496..1608726_NEGATIVE 210 111 72 51 2 NC_003454:FN1969|5end_Hemin_transport_system_permease_protein_hmuU_468211..468441_NEGATIVE 207 158 112 194 143 NC_003454:FN1423|5end_Flavoprotein_2090070..2090300_NEGATIVE 207 110 73 138 95 NC_003454:FN1837|5end_putative_nucleotide-binding_protein_327255..327485_NEGATIVE 206 60 32 49 16 NC_003454:FN1303|5end_Adenosylcobalamin-dependent_DIOL_dehydratase_gamma_subunit_1960284..1960514_NEGATIVE 205 156 112 182 129 NC_003454:FN0301|5end_Iron(III)_dicitrate_transport_system_permease_protein_fecD_935685..935915_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 265 64 23 116 64 NC_003454:FN1969|3end_Hemin_transport_system_permease_protein_hmuU_467186..467336_NEGATIVE 236 80 36 126 70 NC_003454:FN1583|3end_hypothetical_protein_95039..95189_NEGATIVE 234 157 123 134 96 NC_003454:FN0675|3end_60_kDa_chaperonin_GROEL_1330471..1330621_NEGATIVE 230 147 117 137 96 NC_003454:FN1898|3end_Sugar_transport_ATP-binding_protein_384986..385136_NEGATIVE 224 130 81 67 11 NC_003454:FN1532|3end_murein_hydrolase_exporter_44936..45086_NEGATIVE 216 63 21 54 12 NC_003454:FN0239|3end_hypothetical_protein_863923..864073_POSITIVE 210 63 21 67 25 NC_003454:FN0952|3end_cobalamin_biosynthesis_protein_CbiG_1608489..1608639_NEGATIVE 206 60 32 34 1 NC_003454:FN1304|3end_Single-strand_DNA_binding_protein_1960299..1960449_NEGATIVE 206 60 18 91 51 NC_003454:FN1527|3end_hypothetical_protein_42183..42333_NEGATIVE 205 56 16 99 53 NC_003454:FN1782|3end_Phosphocarrier_protein_HPr_264221..264371_NEGATIVE 201 63 21 93 43 NC_003454:FN0592|3end_ATP-dependent_DNA_helicase_pcrA_1247999..1248149_POSITIVE 201 104 66 84 48 NC_003454:FN0119|3end_Flavodoxin_752647..752797_POSITIVE 197 120 75 67 22 NC_003454:FN1680|3end_Transposase_175971..176121_NEGATIVE 197 90 41 137 79 NC_003454:FN1553|3end_Transporter_67150..67300_NEGATIVE 196 60 17 142 98 NC_003454:FN0446|3end_hypothetical_protein_1089404..1089554_POSITIVE 196 129 81 50 5 NC_003454:FN0352|3end_NA+/H+_antiporter_NHAC_985000..985150_POSITIVE 195 96 53 134 87 NC_003454:FN0997|3end_hypothetical_protein_1651384..1651534_NEGATIVE 195 86 41 98 52 NC_003454:FN1538|3end_Arsenical_pump-driving_ATPase_51109..51259_NEGATIVE 194 159 118 65 18 NC_003454:FN0317|3end_tryptophan_synthase_subunit_beta_953819..953969_NEGATIVE 192 47 14 145 108 NC_003454:FN1188|3end_hypothetical_protein_1851357..1851507_POSITIVE