Origin IGS: aaatccccctcctaagaataaaatttactactttcattgtactacaataatttttttaatcaagagaaaaaatacaaatttttagttttaatattaaacaaagtccaaaaaatgtgttaaaataaatataaaataataattataaggggagattagggagaatttaactattggagcctcaattttaataaactttaagttgcaaaagataatgaaataaattataatgaaataaaaaatattgaaatataaaaaaatttaagttacagtaagttacaaaataaaaaatatttgtccttttttatataaaccgacattttattgtcggtttgagtgtcgcttttaataaaacagaaaagaaagtaattgaattttaaatagaaagaataagattgtaattgaataaaatagggagtcttggagggtagaa .........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 ttctaccctccaagactccctattttattcaattacaatcttattctttctatttaaaattcaattactttcttttctgttttattaaaagcgacactcaaaccgacaataaaatgtcggtttatataaaaaaggacaaatattttttattttgtaacttactgtaacttaaatttttttatatttcaatattttttatttcattataatttatttcattatcttttgcaacttaaagtttattaaaattgaggctccaatagttaaattctccctaatctccccttataattattattttatatttattttaacacattttttggactttgtttaatattaaaactaaaaatttgtattttttctcttgattaaaaaaattattgtagtacaatgaaagtagtaaattttattcttaggagggggattt Mask Tandem Repeat Region ================================================ aaatccccctcctaagaataaaatttactactttcattgtactacaataatttttttaatcaagagaaaaaatacaaatttttagttttaatattaaacaaagtccaaaaaatgtgttaaaataaatataaaataataattataaggggagattagggagaatttaactattggagcctcaattttaataaactttaagttgcnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnaatttaagttacagtaagttacaaaataaaaaatatttgtccttttttatataaaccgacattttattgtcggtttgagtgtcgcttttaataaaacagaaaagaaagtaattgaattttaaatagaaagaataagattgtaattgaataaaatagggagtcttggagggtagaa Find is-nt database================================================ Query_seq: FN0829:FN0830|FN0829:FN0830:hypothetical protein:hypothetical protein:<-->:1489964..1490393 430 aaatccccctcctaagaataaaatttactactttcattgtactacaataatttttttaatcaagagaaaaaatacaaatttttagttttaatattaaacaaagtccaaaaaatgtgttaaaataaatataaaataataattataaggggagattagggagaatttaactattggagcctcaattttaataaactttaagttgcaaaagataatgaaataaattataatgaaataaaaaatattgaaatataaaaaaatttaagttacagtaagttacaaaataaaaaatatttgtccttttttatataaaccgacattttattgtcggtttgagtgtcgcttttaataaaacagaaaagaaagtaattgaattttaaatagaaagaataagattgtaattgaataaaatagggagtcttggagggtagaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN0829:FN0830|FN0829:FN0830:hypothetical protein:hypothetical protein:<-->:1489964..1490393 430 aaatccccctcctaagaataaaatttactactttcattgtactacaataatttttttaatcaagagaaaaaatacaaatttttagttttaatattaaacaaagtccaaaaaatgtgttaaaataaatataaaataataattataaggggagattagggagaatttaactattggagcctcaattttaataaactttaagttgcaaaagataatgaaataaattataatgaaataaaaaatattgaaatataaaaaaatttaagttacagtaagttacaaaataaaaaatatttgtccttttttatataaaccgacattttattgtcggtttgagtgtcgcttttaataaaacagaaaagaaagtaattgaattttaaatagaaagaataagattgtaattgaataaaatagggagtcttggagggtagaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN0829:FN0830|FN0829:FN0830:hypothetical protein:hypothetical protein:<-->:1489964..1490393 430 aaatccccctcctaagaataaaatttactactttcattgtactacaataatttttttaatcaagagaaaaaatacaaatttttagttttaatattaaacaaagtccaaaaaatgtgttaaaataaatataaaataataattataaggggagattagggagaatttaactattggagcctcaattttaataaactttaagttgcaaaagataatgaaataaattataatgaaataaaaaatattgaaatataaaaaaatttaagttacagtaagttacaaaataaaaaatatttgtccttttttatataaaccgacattttattgtcggtttgagtgtcgcttttaataaaacagaaaagaaagtaattgaattttaaatagaaagaataagattgtaattgaataaaatagggagtcttggagggtagaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aaatccccctcctaagaataaaatttactactttcattgtactacaataatttttttaatcaagagaaaaaatacaaatttttagttttaatattaaacaaagtccaaaaaatgtgttaaaataaatataaaataataattataaggggagattagggagaatttaactattggagcctcaattttaataaactttaagttgcaaaagataatgaaataaattataatgaaataaaaaatattgaaatataaaaaaatttaagttacagtaagttacaaaataaaaaatatttgtccttttttatataaaccgacattttattgtcggtttgagtgtcgcttttaataaaacagaaaagaaagtaattgaattttaaatagaaagaataagattgtaattgaataaaatagggagtcttggagggtagaa Predict ORF larger than 30AA ================================================ Protein_Len: 46 Strand: - Start: 267 End: 404 .......................................................................................................................................................................................................................................................................... L L N C F L F Y K D K K I Y V S M K N D T Q T D S K I F C F L F Y N F K L Y F S Y S Q L Q M .......................... Protein_Len: 34 Strand: - Start: 188 End: 289 ........................................................................................................................................................................................... Y V K L Q L L Y H F L N Y H F L F Y Q F I F F N L N C Y T V F Y F M ............................................................................................................................................. Protein_Len: 54 Strand: - Start: 97 End: 258 ................................................................................................ V F D L F H T L I F I F Y Y N Y P S I L S F K V I P A E I K I F K L N C F I I F Y I I I F Y F I N F Y L F M ............................................................................................................................................................................ aaatccccctcctaagaataaaatttactactttcattgtactacaataatttttttaatcaagagaaaaaatacaaatttttagttttaatattaaacaaagtccaaaaaatgtgttaaaataaatataaaataataattataaggggagattagggagaatttaactattggagcctcaattttaataaactttaagttgcaaaagataatgaaataaattataatgaaataaaaaatattgaaatataaaaaaatttaagttacagtaagttacaaaataaaaaatatttgtccttttttatataaaccgacattttattgtcggtttgagtgtcgcttttaataaaacagaaaagaaagtaattgaattttaaatagaaagaataagattgtaattgaataaaatagggagtcttggagggtagaa 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: 85 Start: 241 End: 270 ................................................................................................................................................................................................................................................ATTGAAATATAAAAAAATTTAAGTTACAGT................................................................................................................................................................ PromScan Matrix: RpoD-17 Strand: - Score: 84 Start: 139 End: 168 ..........................................................................................................................................GTTAAATTCTCCCTAATCTCCCCTTATAAT...................................................................................................................................................................................................................................................................... PromScan Matrix: RpoD-17 Strand: + Score: 84 Start: 199 End: 228 ......................................................................................................................................................................................................GTTGCAAAAGATAATGAAATAAATTATAAT.......................................................................................................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aaatccccctcctaagaataaaatttactactttcattgtactacaataatttttttaatcaagagaaaaaatacaaatttttagttttaatattaaacaaagtccaaaaaatgtgttaaaataaatataaaataataattataaggggagattagggagaatttaactattggagcctcaattttaataaactttaagttgcaaaagataatgaaataaattataatgaaataaaaaatattgaaatataaaaaaatttaagttacagtaagttacaaaataaaaaatatttgtccttttttatataaaccgacattttattgtcggtttgagtgtcgcttttaataaaacagaaaagaaagtaattgaattttaaatagaaagaataagattgtaattgaataaaatagggagtcttggagggtagaa Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 70 HP_score: -7.0 Tail_Score: -4.03234 Start: 311 End: 328 Full_Region: aaagcgacactcaaa ccgaca ataaaa tgtcgg tttatataaaaaagg ......................................................................................................................................................................................................................................................................................................................ccgacaataaaatgtcgg...................................................................................................... Find igs database================================================ Query_seq: FN0829:FN0830|FN0829:FN0830:hypothetical protein:hypothetical protein:<-->:1489964..1490393 430 aaatccccctcctaagaataaaatttactactttcattgtactacaataatttttttaatcaagagaaaaaatacaaatttttagttttaatattaaacaaagtccaaaaaatgtgttaaaataaatataaaataataattataaggggagattagggagaatttaactattggagcctcaattttaataaactttaagttgcaaaagataatgaaataaattataatgaaataaaaaatattgaaatataaaaaaatttaagttacagtaagttacaaaataaaaaatatttgtccttttttatataaaccgacattttattgtcggtttgagtgtcgcttttaataaaacagaaaagaaagtaattgaattttaaatagaaagaataagattgtaattgaataaaatagggagtcttggagggtagaa Intra-Species Hit: Count: 1 Min: 1 Max: 430 Len: 430 Subject: NC_003454_FN0829_FN0830|hypothetical protein:hypothetical protein|NEGATIVE:POSITIVE|[1489964,1490393]|430 HSP 1 e-value: 2.0E-73 bit: 278.0 Len: 140 Query Start:291 Query End:430 Subject Strand: POSITIVE Subject Start: 291 Subject End: 430 ..................................................................................................................................................................................................................................................................................................tttgtccttttttatataaaccgacattttattgtcggtttgagtgtcgcttttaataaaacagaaaagaaagtaattgaattttaaatagaaagaataagattgtaattgaataaaatagggagtcttggagggtagaa ..................................................................................................................................................................................................................................................................................................tttgtccttttttatataaaccgacattttattgtcggtttgagtgtcgcttttaataaaacagaaaagaaagtaattgaattttaaatagaaagaataagattgtaattgaataaaatagggagtcttggagggtagaa HSP 2 e-value: 8.0E-20 bit: 99.6 Len: 50 Query Start:1 Query End:50 Subject Strand: POSITIVE Subject Start: 1 Subject End: 50 aaatccccctcctaagaataaaatttactactttcattgtactacaataa............................................................................................................................................................................................................................................................................................................................................................................................ aaatccccctcctaagaataaaatttactactttcattgtactacaataa............................................................................................................................................................................................................................................................................................................................................................................................ HSP 3 e-value: 7.0E-11 bit: 69.9 Len: 35 Query Start:146 Query End:180 Subject Strand: POSITIVE Subject Start: 146 Subject End: 180 .................................................................................................................................................ggggagattagggagaatttaactattggagcctc.......................................................................................................................................................................................................................................................... .................................................................................................................................................ggggagattagggagaatttaactattggagcctc.......................................................................................................................................................................................................................................................... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAUCCCCCUCCUAAGAAUAAAAUUUACUACUUUCAUUGUACUACAAUAAUUUUUUUAAUCAAGAGAAAAAAUACAAAUUUUUAGUUUUAAUAUUAAACAAAGUCCAAAAAAUGUGUUAAAAUAAAUAUAAAAUAAUAAUUAUAAGGGGAGAUUAGGGAGAAUUUAACUAUUGGAGCCUCAAUUUUAAUAAACUUUAAGUUGCAAAAGAUAAUGAAAUAAAUUAUAAUGAAAUAAAAAAUAUUGAAAUAUAAAAAAAUUUAAGUUACAGUAAGUUACAAAAUAAAAAAUAUUUGUCCUUUUUUAUAUAAACCGACAUUUUAUUGUCGGUUUGAGUGUCGCUUUUAAUAAAACAGAAAAGAAAGUAAUUGAAUUUUAAAUAGAAAGAAUAAGAUUGUAAUUGAAUAAAAUAGGGAGUCUUGGAGGGUAGAA ......((((((......(((((((((.(((((((..((((..((...((((((((((.........((((((....)))))).(((((((((((........(((((....((((((......))))))...............((..(((((......)))))..)).)))))......((((((...(((.....))).......(((((.......)))))..))))))....))))))))))).))))))))))...))))))..((((.(((..((((((((.........)))))))).((((((((((......))))))))))..))).))))................)))))))..)))))))))............((((((.(.(((......)))..).))))))))))))..... (-69.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUCUACCCUCCAAGACUCCCUAUUUUAUUCAAUUACAAUCUUAUUCUUUCUAUUUAAAAUUCAAUUACUUUCUUUUCUGUUUUAUUAAAAGCGACACUCAAACCGACAAUAAAAUGUCGGUUUAUAUAAAAAAGGACAAAUAUUUUUUAUUUUGUAACUUACUGUAACUUAAAUUUUUUUAUAUUUCAAUAUUUUUUAUUUCAUUAUAAUUUAUUUCAUUAUCUUUUGCAACUUAAAGUUUAUUAAAAUUGAGGCUCCAAUAGUUAAAUUCUCCCUAAUCUCCCCUUAUAAUUAUUAUUUUAUAUUUAUUUUAACACAUUUUUUGGACUUUGUUUAAUAUUAAAACUAAAAAUUUGUAUUUUUUCUCUUGAUUAAAAAAAUUAUUGUAGUACAAUGAAAGUAGUAAAUUUUAUUCUUAGGAGGGGGAUUU .(((.((((((((((..........((......))...................(((((((..(((((((((.(((..((((((......((((.....(((((((((......)))))))))..((((((((....((((((.....((((.((.((.....)).))..))))......)))))).....))))))))..........................))))...........(((((((...((((.(((((..((((((..................(((((........))))).....)))))).......))))))))).))))))).))))))..)))..(((((((....(...(((((.....)))))..).))))))).))))))))).))))))).)))).)))))))))... (-62.10) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 740 50 1 141 92 NC_003454:FN0829|5end_hypothetical_protein_1489873..1490103_NEGATIVE 242 340 298 212 174 NC_003454:FN1505|5end_6,7-dimethyl-8-ribityllumazine_synthase_10396..10626_POSITIVE 240 44 8 133 97 NC_003454:FN1800|5end_Peptidyl-prolyl_cis-trans_isomerase_281630..281860_POSITIVE 227 189 142 191 137 NC_003454:FN1838|5end_Glycerol_uptake_facilitator_protein_327489..327719_POSITIVE 215 335 298 229 196 NC_003454:FN1498|5end_Integral_membrane_protein_2563..2793_POSITIVE 211 339 295 140 99 NC_003454:FN0630|5end_PTS_system,_IIC_component_1289857..1290087_NEGATIVE 206 204 170 51 12 NC_003454:FN1424|5end_ACYL-COA_dehydrogenase,_short-chain_specific_2092005..2092235_NEGATIVE 201 215 176 73 27 NC_003454:FN0886|5end_Hemin_receptor_1545768..1545998_POSITIVE 201 358 316 67 24 NC_003454:FN1596|5end_Nitrogen_fixation_iron-sulphur_protein_RNFC_107178..107408_NEGATIVE 200 70 24 202 151 NC_003454:FN1024|5end_DNA-binding_protein_HU_1678480..1678710_NEGATIVE 194 23 3 86 63 NC_003454:FN0864|5end_hypothetical_protein_1522900..1523130_NEGATIVE 194 426 395 39 7 NC_003454:FN0184|5end_hypothetical_protein_809087..809317_NEGATIVE 192 155 111 212 158 NC_003454:FN0508|5end_Serine_protease_1158652..1158882_NEGATIVE 192 44 4 57 18 NC_003454:FN0381|5end_hypothetical_protein_1012348..1012578_POSITIVE 190 44 3 124 86 NC_003454:FN0209|5end_Hypothetical_cytosolic_protein_836127..836357_POSITIVE 189 160 113 229 190 NC_003454:FN0814|5end_Propionate_CoA-transferase_1472717..1472947_POSITIVE 189 71 33 98 64 NC_003454:FN2093|5end_General_secretion_pathway_protein_G_603551..603781_NEGATIVE 188 37 7 136 97 NC_003454:FN0810|5end_Low-specificity_threonine_aldolase_1469038..1469268_POSITIVE 187 305 262 63 14 NC_003454:FN0342|5end_Peptidyl-prolyl_cis-trans_isomerase_975925..976155_NEGATIVE 186 428 384 201 161 NC_003454:FN0042|5end_Rod_shape-determining_protein_rodA_682129..682359_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 240 44 8 73 37 NC_003454:FN1799|3end_Spermidine/putrescine_transport_system_permease_protein_potC_281650..281800_POSITIVE 211 426 383 56 7 NC_003454:FN1460|3end_Hypothetical_cytosolic_protein_2141682..2141832_POSITIVE 211 339 295 129 88 NC_003454:FN0631|3end_PTS_system,_IIB_component_1289868..1290018_NEGATIVE 203 120 77 147 101 NC_003454:FN1659|3end_hypothetical_protein_155826..155976_POSITIVE 200 70 24 58 7 NC_003454:FN1025|3end_Guanine-hypoxanthine_permease_1678624..1678774_NEGATIVE 190 44 3 113 75 NC_003454:FN0208|3end_(R)-2-hydroxyglutaryl-CoA_dehydratase_beta-subunit_836196..836346_POSITIVE 188 37 7 125 86 NC_003454:FN0809|3end_23S_rRNA_methyltransferase_1469107..1469257_POSITIVE 184 332 294 123 83 NC_003454:FN0416|3end_Type_III_restriction-modification_system_methylation_subunit_1055957..1056107_POSITIVE 184 48 9 68 30 NC_003454:FN0059|3end_NifU_protein_695619..695769_POSITIVE 184 40 6 113 77 NC_003454:FN1786|3end_ADP-heptose_synthase_267821..267971_POSITIVE 183 209 173 75 34 NC_003454:FN0798|3end_Fructose-1,6-bisphosphatase_1457852..1458002_POSITIVE 180 339 294 75 26 NC_003454:FN1712|3end_hypothetical_protein_207608..207758_POSITIVE 180 175 152 137 115 NC_003454:FN1639|3end_SSU_ribosomal_protein_S3P_137504..137654_NEGATIVE 179 185 143 130 76 NC_003454:FN0551|3end_Bacterial_regulatory_proteins,_crp_family_1203649..1203799_POSITIVE 179 41 4 67 24 NC_003454:FN1579|3end_Cysteinyl-tRNA_synthetase_88784..88934_NEGATIVE 178 41 6 136 105 NC_003454:FN0016|3end_hypothetical_protein_654366..654516_POSITIVE 176 183 146 42 2 NC_003454:FN1503|3end_Nickel_transport_system_permease_protein_nikB_7503..7653_NEGATIVE 175 48 3 120 85 NC_003454:FN0041|3end_hypothetical_protein_680619..680769_NEGATIVE 174 179 144 63 30 NC_003454:FN1421|3end_Pyruvate-flavodoxin_oxidoreductase_2086957..2087107_POSITIVE 174 30 3 134 101 NC_003454:FN0595|3end_UDP-N-acetylglucosamine_acyltransferase_1250081..1250231_POSITIVE