Origin IGS: tttttcacctcacactttacttattaaatatattttactctaattttataaaaattgtaacatttgttacagaaaaaactttacaagaattatataatttactaaaataataaagaaatgaaatgtagattgagatttaaaaggagaagttaaaatgtatataagcaaatcaatgtcaataaaatcaatagtggagaaatatccagaaacaatacctgttttcacaaatattgggtttaaaggtttagataatccagcagttttacaaaaactagaagaacaaaatataacattggaaaaagcaatgatgataaaaaaagaagatgtagatgcttttattccaatgttacaacaggcaatagcatctgttgaaagagaagatgaagga .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tccttcatcttctctttcaacagatgctattgcctgttgtaacattggaataaaagcatctacatcttctttttttatcatcattgctttttccaatgttatattttgttcttctagtttttgtaaaactgctggattatctaaacctttaaacccaatatttgtgaaaacaggtattgtttctggatatttctccactattgattttattgacattgatttgcttatatacattttaacttctccttttaaatctcaatctacatttcatttctttattattttagtaaattatataattcttgtaaagttttttctgtaacaaatgttacaatttttataaaattagagtaaaatatatttaataagtaaagtgtgaggtgaaaaa Mask Tandem Repeat Region ================================================ tttttcacctcacactttacttattaaatatattttactctaattttataaaaattgtaacatttgttacagaaaaaactttacaagaattatataatttactaaaataataaagaaatgaaatgtagattgagatttaaaaggagaagttaaaatgtatataagcaaatcaatgtcaataaaatcaatagtggagaaatatccagaaacaatacctgttttcacaaatattgggtttaaaggtttagataatccagcagttttacaaaaactagaagaacaaaatataacattggaaaaagcaatgatgataaaaaaagaagatgtagatgcttttattccaatgttacaacaggcaatagcatctgttgaaagagaagatgaagga Find is-nt database================================================ Query_seq: FN0127:FN0128|FN0127:FN0128:Fe-S oxidoreductase:Spermidine/putrescine-binding protein:<-->:756403..756790 388 tttttcacctcacactttacttattaaatatattttactctaattttataaaaattgtaacatttgttacagaaaaaactttacaagaattatataatttactaaaataataaagaaatgaaatgtagattgagatttaaaaggagaagttaaaatgtatataagcaaatcaatgtcaataaaatcaatagtggagaaatatccagaaacaatacctgttttcacaaatattgggtttaaaggtttagataatccagcagttttacaaaaactagaagaacaaaatataacattggaaaaagcaatgatgataaaaaaagaagatgtagatgcttttattccaatgttacaacaggcaatagcatctgttgaaagagaagatgaagga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN0127:FN0128|FN0127:FN0128:Fe-S oxidoreductase:Spermidine/putrescine-binding protein:<-->:756403..756790 388 tttttcacctcacactttacttattaaatatattttactctaattttataaaaattgtaacatttgttacagaaaaaactttacaagaattatataatttactaaaataataaagaaatgaaatgtagattgagatttaaaaggagaagttaaaatgtatataagcaaatcaatgtcaataaaatcaatagtggagaaatatccagaaacaatacctgttttcacaaatattgggtttaaaggtttagataatccagcagttttacaaaaactagaagaacaaaatataacattggaaaaagcaatgatgataaaaaaagaagatgtagatgcttttattccaatgttacaacaggcaatagcatctgttgaaagagaagatgaagga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN0127:FN0128|FN0127:FN0128:Fe-S oxidoreductase:Spermidine/putrescine-binding protein:<-->:756403..756790 388 tttttcacctcacactttacttattaaatatattttactctaattttataaaaattgtaacatttgttacagaaaaaactttacaagaattatataatttactaaaataataaagaaatgaaatgtagattgagatttaaaaggagaagttaaaatgtatataagcaaatcaatgtcaataaaatcaatagtggagaaatatccagaaacaatacctgttttcacaaatattgggtttaaaggtttagataatccagcagttttacaaaaactagaagaacaaaatataacattggaaaaagcaatgatgataaaaaaagaagatgtagatgcttttattccaatgttacaacaggcaatagcatctgttgaaagagaagatgaagga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tttttcacctcacactttacttattaaatatattttactctaattttataaaaattgtaacatttgttacagaaaaaactttacaagaattatataatttactaaaataataaagaaatgaaatgtagattgagatttaaaaggagaagttaaaatgtatataagcaaatcaatgtcaataaaatcaatagtggagaaatatccagaaacaatacctgttttcacaaatattgggtttaaaggtttagataatccagcagttttacaaaaactagaagaacaaaatataacattggaaaaagcaatgatgataaaaaaagaagatgtagatgcttttattccaatgttacaacaggcaatagcatctgttgaaagagaagatgaagga Predict ORF larger than 30AA ================================================ Protein_Len: 60 Strand: + Start: 155 End: 388 .......................................................................................................................................................... M Y I S K S M S I K S I V E K Y P E T I P V F T N I G F K G L D N P A V L Q K L E E Q N I T L E K A M M I K K E D V D A Protein_Len: 60 Strand: - Start: 70 End: 360 ..................................................................... F D I T S F Y G S V I G T K V F I P N L P K S L G A T K C F S S S C F I V N S F A I I I F F S S T S A K I G I N C C A M ............................ Protein_Len: 33 Strand: - Start: 38 End: 136 ..................................... E L K I F I T V N T V S F V K C S N Y L K S F Y Y L F S I Y I S M ............................................................................................................................................................................................................................................................ tttttcacctcacactttacttattaaatatattttactctaattttataaaaattgtaacatttgttacagaaaaaactttacaagaattatataatttactaaaataataaagaaatgaaatgtagattgagatttaaaaggagaagttaaaatgtatataagcaaatcaatgtcaataaaatcaatagtggagaaatatccagaaacaatacctgttttcacaaatattgggtttaaaggtttagataatccagcagttttacaaaaactagaagaacaaaatataacattggaaaaagcaatgatgataaaaaaagaagatgtagatgcttttattccaatgttacaacaggcaatagcatctgttgaaagagaagatgaagga 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: 83 Start: 79 End: 108 ..............................................................................CTTTACAAGAATTATATAATTTACTAAAAT........................................................................................................................................................................................................................................................................................ PromScan Matrix: RpoD-17 Strand: - Score: 81 Start: 32 End: 61 ...............................GTTACAATTTTTATAAAATTAGAGTAAAAT....................................................................................................................................................................................................................................................................................................................................... PromScan Matrix: RpoD-17 Strand: - Score: 81 Start: 89 End: 118 ........................................................................................TTTCTTTATTATTTTAGTAAATTATATAAT.............................................................................................................................................................................................................................................................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tttttcacctcacactttacttattaaatatattttactctaattttataaaaattgtaacatttgttacagaaaaaactttacaagaattatataatttactaaaataataaagaaatgaaatgtagattgagatttaaaaggagaagttaaaatgtatataagcaaatcaatgtcaataaaatcaatagtggagaaatatccagaaacaatacctgttttcacaaatattgggtttaaaggtttagataatccagcagttttacaaaaactagaagaacaaaatataacattggaaaaagcaatgatgataaaaaaagaagatgtagatgcttttattccaatgttacaacaggcaatagcatctgttgaaagagaagatgaagga Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: FN0127:FN0128|FN0127:FN0128:Fe-S oxidoreductase:Spermidine/putrescine-binding protein:<-->:756403..756790 388 tttttcacctcacactttacttattaaatatattttactctaattttataaaaattgtaacatttgttacagaaaaaactttacaagaattatataatttactaaaataataaagaaatgaaatgtagattgagatttaaaaggagaagttaaaatgtatataagcaaatcaatgtcaataaaatcaatagtggagaaatatccagaaacaatacctgttttcacaaatattgggtttaaaggtttagataatccagcagttttacaaaaactagaagaacaaaatataacattggaaaaagcaatgatgataaaaaaagaagatgtagatgcttttattccaatgttacaacaggcaatagcatctgttgaaagagaagatgaagga Intra-Species Hit: Count: 1 Min: 1 Max: 388 Len: 388 Subject: NC_003454_FN0127_FN0128|Fe-S oxidoreductase:Spermidine/putrescine-binding protein|NEGATIVE:POSITIVE|[756403,756790]|388 HSP 1 e-value: 0.0 bit: 728.0 Len: 388 Query Start:1 Query End:388 Subject Strand: POSITIVE Subject Start: 1 Subject End: 388 tttttcacctcacactttacttattaaatatattttactctaattttataaaaattgtaacatttgttacagaaaaaactttacaagaattatataatttactaaaataataaagaaatgaaatgtagattgagatttaaaaggagaagttaaaatgtatataagcaaatcaatgtcaataaaatcaatagtggagaaatatccagaaacaatacctgttttcacaaatattgggtttaaaggtttagataatccagcagttttacaaaaactagaagaacaaaatataacattggaaaaagcaatgatgatnnnnnnngaagatgtagatgcttttattccaatgttacaacaggcaatagcatctgttgaaagagaagatgaagga tttttcacctcacactttacttattaaatatattttactctaattttataaaaattgtaacatttgttacagaaaaaactttacaagaattatataatttactaaaataataaagaaatgaaatgtagattgagatttaaaaggagaagttaaaatgtatataagcaaatcaatgtcaataaaatcaatagtggagaaatatccagaaacaatacctgttttcacaaatattgggtttaaaggtttagataatccagcagttttacaaaaactagaagaacaaaatataacattggaaaaagcaatgatgataaaaaaagaagatgtagatgcttttattccaatgttacaacaggcaatagcatctgttgaaagagaagatgaagga Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUUUCACCUCACACUUUACUUAUUAAAUAUAUUUUACUCUAAUUUUAUAAAAAUUGUAACAUUUGUUACAGAAAAAACUUUACAAGAAUUAUAUAAUUUACUAAAAUAAUAAAGAAAUGAAAUGUAGAUUGAGAUUUAAAAGGAGAAGUUAAAAUGUAUAUAAGCAAAUCAAUGUCAAUAAAAUCAAUAGUGGAGAAAUAUCCAGAAACAAUACCUGUUUUCACAAAUAUUGGGUUUAAAGGUUUAGAUAAUCCAGCAGUUUUACAAAAACUAGAAGAACAAAAUAUAACAUUGGAAAAAGCAAUGAUGAUAAAAAAAGAAGAUGUAGAUGCUUUUAUUCCAAUGUUACAACAGGCAAUAGCAUCUGUUGAAAGAGAAGAUGAAGGA (((((((.(((........(((((...((((((((((((((..(((((......(((((((....)))))))......................((((((((......................)))))))).....)))))..)).)).)))))))))))))))...................(((((((((((......)))).........(((((((((.......(((((((.............))))))).(((((.....))))).)))..........(((((((((((((((((...((................))...))))))..))))))))))).)))))).........)))))))..)))....))))))) (-65.16) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCCUUCAUCUUCUCUUUCAACAGAUGCUAUUGCCUGUUGUAACAUUGGAAUAAAAGCAUCUACAUCUUCUUUUUUUAUCAUCAUUGCUUUUUCCAAUGUUAUAUUUUGUUCUUCUAGUUUUUGUAAAACUGCUGGAUUAUCUAAACCUUUAAACCCAAUAUUUGUGAAAACAGGUAUUGUUUCUGGAUAUUUCUCCACUAUUGAUUUUAUUGACAUUGAUUUGCUUAUAUACAUUUUAACUUCUCCUUUUAAAUCUCAAUCUACAUUUCAUUUCUUUAUUAUUUUAGUAAAUUAUAUAAUUCUUGUAAAGUUUUUUCUGUAACAAAUGUUACAAUUUUUAUAAAAUUAGAGUAAAAUAUAUUUAAUAAGUAAAGUGUGAGGUGAAAAA ...(((((((((.((((((((((..((....))))))))..(((((((((..((((((..........................)))))))))))))))(((((((((...((((((((((.((((((.(((.(((((((.(((....(((((..((((((((((....))))))))))....((((......)))).....(((((....((..((((..((........))..))))..)).......)))))...........................)))))....))).)))))))..)))..........((((((....))))))..)))))))))))))))))))))))))..........)))).).))))))))... (-71.57) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 625 50 1 141 92 NC_003454:FN0127|5end_Fe-S_oxidoreductase_756312..756542_NEGATIVE 292 380 333 216 172 NC_003454:FN1923|5end_Adenine-specific_methyltransferase_421097..421327_NEGATIVE 242 261 224 74 36 NC_003454:FN1593|5end_NADH-ubiquinone_oxidoreductase_104360..104590_NEGATIVE 228 269 221 54 3 NC_003454:FN2021|5end_ABC1_family_protein_525079..525309_NEGATIVE 225 370 322 62 14 NC_003454:FN0964|5end_Precorrin-8W_decarboxylase_1618306..1618536_NEGATIVE 225 224 189 152 114 NC_003454:FN1955|5end_hypothetical_protein_459936..460166_POSITIVE 222 348 306 224 177 NC_003454:FN0951|5end_Precorrin-3B_C17-methyltransferase_1608496..1608726_NEGATIVE 216 374 333 212 174 NC_003454:FN0195|5end_Dipeptide_transport_ATP-binding_protein_dppD_820558..820788_POSITIVE 211 367 328 190 146 NC_003454:FN1019|5end_3-hydroxybutyryl-CoA_dehydrogenase_1673784..1674014_NEGATIVE 208 378 331 73 11 NC_003454:FN1825|5end_hypothetical_protein_313994..314224_POSITIVE 206 373 331 62 26 NC_003454:FN1192|5end_hypothetical_protein_1854679..1854909_POSITIVE 206 367 322 169 127 NC_003454:FN0409|5end_Acetyl-coenzyme_A_carboxylase_carboxyl_transferase_subunit_alpha_1046277..1046507_POSITIVE 205 368 328 133 93 NC_003454:FN1448|5end_Hypothetical_cytosolic_protein_2118428..2118658_NEGATIVE 205 274 231 149 104 NC_003454:FN1269|5end_Hypothetical_lipoprotein_1926242..1926472_NEGATIVE 205 373 331 198 159 NC_003454:FN1506|5end_5-amino-6-(5-phosphoribosylamino)uracil_reductase_10871..11101_POSITIVE 201 110 65 78 38 NC_003454:FN0941|5end_Gamma-glutamyltranspeptidase_1595266..1595496_NEGATIVE 201 205 161 150 99 NC_003454:FN0727|5end_hypothetical_protein_1385507..1385737_NEGATIVE 201 178 139 56 23 NC_003454:FN0527|5end_Alanyl-tRNA_synthetase_1184098..1184328_NEGATIVE 201 380 331 145 91 NC_003454:FN0479|5end_RNA_polymerase_sigma-E_factor_1127003..1127233_POSITIVE 200 315 271 101 62 NC_003454:FN0144|5end_hypothetical_protein_774353..774583_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 261 370 331 41 3 NC_003454:FN1998|3end_HIPA_protein_500391..500541_POSITIVE 242 261 224 74 36 NC_003454:FN1594|3end_Nitrogen_fixation_protein_RNFG_104360..104510_NEGATIVE 234 265 232 54 5 NC_003454:FN1260|3end_Sensory_Transduction_Protein_Kinase_1915863..1916013_NEGATIVE 228 269 221 61 10 NC_003454:FN2022|3end_transcription_elongation_factor_NusA_525072..525222_NEGATIVE 220 372 331 43 4 NC_003454:FN0965|3end_D-3-phosphoglycerate_dehydrogenase_1618328..1618478_NEGATIVE 205 274 231 65 20 NC_003454:FN1270|3end_Hypothetical_cytosolic_protein_1926326..1926476_NEGATIVE 201 380 331 89 35 NC_003454:FN0478|3end_GcpE_protein_1127027..1127177_POSITIVE 199 224 187 69 32 NC_003454:FN0155|3end_hypothetical_protein_784462..784612_POSITIVE 192 363 324 57 24 NC_003454:FN0382|3end_hypothetical_protein_1014224..1014374_POSITIVE 190 349 325 67 42 NC_003454:FN1440|3end_1-phosphofructokinase_2108262..2108412_POSITIVE 190 222 181 85 41 NC_003454:FN0595|3end_UDP-N-acetylglucosamine_acyltransferase_1250081..1250231_POSITIVE 188 239 210 63 31 NC_003454:FN0490|3end_Integral_membrane_protein_1135452..1135602_NEGATIVE 187 225 195 137 106 NC_003454:FN1555|3end_Protein_Translation_Elongation_Factor_Tu_76252..76402_NEGATIVE 186 274 231 113 70 NC_003454:FN2039|3end_50S_ribosomal_protein_L1_547850..548000_NEGATIVE 186 368 327 45 7 NC_003454:FN1737|3end_V-type_ATP_synthase_subunit_F_236039..236189_NEGATIVE 185 178 131 93 50 NC_003454:FN0427|3end_Orotate_phosphoribosyltransferase_1070120..1070270_POSITIVE 184 367 333 115 82 NC_003454:FN1482|3end_Guanosine-3',5'-bis(Diphosphate)_3'-pyrophosphohydrolase_2163815..2163965_NEGATIVE 184 379 333 67 14 NC_003454:FN0854|3end_Glucose-1-phosphate_adenylyltransferase_1512324..1512474_NEGATIVE 183 204 161 120 77 NC_003454:FN1403|3end_Histidine_permease_2063133..2063283_POSITIVE 179 258 215 117 59 NC_003454:FN0314|3end_Caffeoyl-CoA_O-methyltransferase_951931..952081_POSITIVE