Origin IGS: gacattacctcttatatatttagattacttgctactattatatcataaaagcagatgatagggcttagagcggaggatttgcctgattttcaaaagaatagtattgtttttgaaaaaacagataaaaaacagatagcgggtaggaaggggatagatggctttgttagaatagaattgttcaaaaaaacaattactgtcaggaagcaacaaacttcctgcttgctaaataaaggagaaatcaa .........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 ttgatttctcctttatttagcaagcaggaagtttgttgcttcctgacagtaattgtttttttgaacaattctattctaacaaagccatctatccccttcctacccgctatctgttttttatctgttttttcaaaaacaatactattcttttgaaaatcaggcaaatcctccgctctaagccctatcatctgcttttatgatataatagtagcaagtaatctaaatatataagaggtaatgtc Mask Tandem Repeat Region ================================================ gacattacctcttatatatttagattacttgctactattatatcataaaagcagatgatagggcttagagcggaggatttgcctgattttcaaaagaatagtattgtttttgaaaaaacagataaaaaacagatagcgggtaggaaggggatagatggctttgttagaatagaattgttcaaaaaaacaattactgtcaggaagcaacaaacttcctgcttgctaaataaaggagaaatcaa Find is-nt database================================================ Query_seq: SSA_0891:SSA_0892|SSA_0891:SSA_0892:3-carboxymuconate cyclase, putative:ATP-binding cassette lipoprotein, putative:<-->:884124..884365 242 gacattacctcttatatatttagattacttgctactattatatcataaaagcagatgatagggcttagagcggaggatttgcctgattttcaaaagaatagtattgtttttgaaaaaacagataaaaaacagatagcgggtaggaaggggatagatggctttgttagaatagaattgttcaaaaaaacaattactgtcaggaagcaacaaacttcctgcttgctaaataaaggagaaatcaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0891:SSA_0892|SSA_0891:SSA_0892:3-carboxymuconate cyclase, putative:ATP-binding cassette lipoprotein, putative:<-->:884124..884365 242 gacattacctcttatatatttagattacttgctactattatatcataaaagcagatgatagggcttagagcggaggatttgcctgattttcaaaagaatagtattgtttttgaaaaaacagataaaaaacagatagcgggtaggaaggggatagatggctttgttagaatagaattgttcaaaaaaacaattactgtcaggaagcaacaaacttcctgcttgctaaataaaggagaaatcaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0891:SSA_0892|SSA_0891:SSA_0892:3-carboxymuconate cyclase, putative:ATP-binding cassette lipoprotein, putative:<-->:884124..884365 242 gacattacctcttatatatttagattacttgctactattatatcataaaagcagatgatagggcttagagcggaggatttgcctgattttcaaaagaatagtattgtttttgaaaaaacagataaaaaacagatagcgggtaggaaggggatagatggctttgttagaatagaattgttcaaaaaaacaattactgtcaggaagcaacaaacttcctgcttgctaaataaaggagaaatcaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gacattacctcttatatatttagattacttgctactattatatcataaaagcagatgatagggcttagagcggaggatttgcctgattttcaaaagaatagtattgtttttgaaaaaacagataaaaaacagatagcgggtaggaaggggatagatggctttgttagaatagaattgttcaaaaaaacaattactgtcaggaagcaacaaacttcctgcttgctaaataaaggagaaatcaa Predict ORF larger than 30AA ================================================ Protein_Len: 60 Strand: + Start: 55 End: 240 ...................................................... M I G L R A E D L P D F Q K N S I V F E K T D K K Q I A G R K G I D G F V R I E L F K K T I T V R K Q Q T S C L L N K G .. Protein_Len: 50 Strand: - Start: 93 End: 242 ............................................................................................ F F L I T K S F V S L F C I A P L F P I S P K T L I S N N L F V I V T L F C C V E Q K S F L P S I M Protein_Len: 55 Strand: - Start: 46 End: 210 ............................................. L L L H Y P K S R L I Q R I K L L I T N N K F F C I F F L Y R T P L P Y I A K N S Y F Q E F F C N S D P L L M ................................ gacattacctcttatatatttagattacttgctactattatatcataaaagcagatgatagggcttagagcggaggatttgcctgattttcaaaagaatagtattgtttttgaaaaaacagataaaaaacagatagcgggtaggaaggggatagatggctttgttagaatagaattgttcaaaaaaacaattactgtcaggaagcaacaaacttcctgcttgctaaataaaggagaaatcaa 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================================================ gacattacctcttatatatttagattacttgctactattatatcataaaagcagatgatagggcttagagcggaggatttgcctgattttcaaaagaatagtattgtttttgaaaaaacagataaaaaacagatagcgggtaggaaggggatagatggctttgttagaatagaattgttcaaaaaaacaattactgtcaggaagcaacaaacttcctgcttgctaaataaaggagaaatcaa Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 48 HP_score: -3.4 Tail_Score: -3.18264 Start: 197 End: 219 Full_Region: AAAAAACAATTACTG TCAGGAAG CAACAAA CTTCCTGC TTGCTAAATAAAGGA ....................................................................................................................................................................................................TCAGGAAGCAACAAACTTCCTGC....................... TransTerm Strand: + Conf: 59 HP_score: -6.9 Tail_Score: -2.50816 Start: 198 End: 218 Full_Region: AAAAACAATTACTGT CAGGAAG CAACAAA CTTCCTG CTTGCTAAATAAAGG .....................................................................................................................................................................................................CAGGAAGCAACAAACTTCCTG........................ TransTerm Strand: + Conf: 45 HP_score: -3.7 Tail_Score: -2.79098 Start: 200 End: 216 Full_Region: AAACAATTACTGTCA GGAAG CAACAAA CTTCC TGCTTGCTAAATAAA .......................................................................................................................................................................................................GGAAGCAACAAACTTCC.......................... Find igs database================================================ Query_seq: SSA_0891:SSA_0892|SSA_0891:SSA_0892:3-carboxymuconate cyclase, putative:ATP-binding cassette lipoprotein, putative:<-->:884124..884365 242 gacattacctcttatatatttagattacttgctactattatatcataaaagcagatgatagggcttagagcggaggatttgcctgattttcaaaagaatagtattgtttttgaaaaaacagataaaaaacagatagcgggtaggaaggggatagatggctttgttagaatagaattgttcaaaaaaacaattactgtcaggaagcaacaaacttcctgcttgctaaataaaggagaaatcaa Intra-Species Hit: Count: 1 Min: 1 Max: 242 Len: 242 Subject: NC_009009_SSA_0891_SSA_0892|3-carboxymuconate cyclase, putative:ATP-binding cassette lipoprotein, putative|NEGATIVE:POSITIVE|[884124,884365]|242 HSP 1 e-value: 1.0E-122 bit: 438.0 Len: 242 Query Start:1 Query End:242 Subject Strand: POSITIVE Subject Start: 1 Subject End: 242 gacattacctcttatatatttagattacttgctactattatatcataaaagcagatgatagggcttagagcggaggatttgcctgattttcaaaagaatagtattgtttttgaaaaaacagataaaaaacagatagcgggtaggaaggggatagatggctttgttagaatagaattgttcnnnnnnncaattactgtcaggaagcaacaaacttcctgcttgctaaataaaggagaaatcaa gacattacctcttatatatttagattacttgctactattatatcataaaagcagatgatagggcttagagcggaggatttgcctgattttcaaaagaatagtattgtttttgaaaaaacagataaaaaacagatagcgggtaggaaggggatagatggctttgttagaatagaattgttcaaaaaaacaattactgtcaggaagcaacaaacttcctgcttgctaaataaaggagaaatcaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GACAUUACCUCUUAUAUAUUUAGAUUACUUGCUACUAUUAUAUCAUAAAAGCAGAUGAUAGGGCUUAGAGCGGAGGAUUUGCCUGAUUUUCAAAAGAAUAGUAUUGUUUUUGAAAAAACAGAUAAAAAACAGAUAGCGGGUAGGAAGGGGAUAGAUGGCUUUGUUAGAAUAGAAUUGUUCAAAAAAACAAUUACUGUCAGGAAGCAACAAACUUCCUGCUUGCUAAAUAAAGGAGAAAUCAA ........(((((.(((...((((((..(((((.(((...((((((........)))))).....))))))))..)))))).(((.((((((((((.(......).))))))))))..)))............((((((((((((((..........(((((.(..((.((((((((((......))))))).)))))).)))))......)))))))))))))).))).)))))....... (-56.79) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUGAUUUCUCCUUUAUUUAGCAAGCAGGAAGUUUGUUGCUUCCUGACAGUAAUUGUUUUUUUGAACAAUUCUAUUCUAACAAAGCCAUCUAUCCCCUUCCUACCCGCUAUCUGUUUUUUAUCUGUUUUUUCAAAAACAAUACUAUUCUUUUGAAAAUCAGGCAAAUCCUCCGCUCUAAGCCCUAUCAUCUGCUUUUAUGAUAUAAUAGUAGCAAGUAAUCUAAAUAUAUAAGAGGUAAUGUC ...((((((....(((((((....((((((((.....))))))))..((.((((((((....))))))))))............................(((..((((.(((((.(((..(((..(((((((((............))))))))).)))..)))......((.....))..((((((........)))))).)))))))))..)))..)))))))....))))))...... (-44.70) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 906 100 51 191 142 NC_009009:SSA_0891|5end_3-carboxymuconate_cyclase,_putative_884033..884263_NEGATIVE 322 164 128 224 190 NC_009009:SSA_0089|5end_V-type_sodium_ATPase,_subunit_F,_putative_89930..90160_POSITIVE 320 77 32 159 116 NC_009009:SSA_1824|5end_hypothetical_protein_1812746..1812976_NEGATIVE 302 86 50 203 164 NC_009009:SSA_1653|5end_hypothetical_protein_1651371..1651601_NEGATIVE 291 168 127 151 107 NC_009009:SSA_0017|5end_Cell_shape_determining_protein_MreC,_putative_22811..23041_POSITIVE 285 85 51 229 198 NC_009009:SSA_0273|5end_hypothetical_protein_267071..267301_POSITIVE 284 79 31 195 148 NC_009009:SSA_0923|5end_Transcriptional_regulator,_TetR/AcrR_family,_putative_933010..933240_POSITIVE 283 85 41 194 140 NC_009009:SSA_1595|5end_Tellurite_resistance,_putative_1601814..1602044_NEGATIVE 282 86 48 222 190 NC_009009:SSA_0220|5end_PTS_system,_mannose-specific_IIB_component,_putative_215848..216078_POSITIVE 281 79 35 158 116 NC_009009:SSA_1172|5end_hypothetical_protein_1199926..1200156_NEGATIVE 281 174 131 65 19 NC_009009:SSA_1115|5end_Cytochrome_C-type_biogenesis_protein,_putative_1141614..1141844_POSITIVE 281 177 135 192 135 NC_009009:SSA_0252|5end_hypothetical_protein_245839..246069_NEGATIVE 280 165 121 83 29 NC_009009:SSA_1049|5end_ABC_transporter_membrane-spanning_permease-spermidine/putrescine_transport,_putative_1064085..1064315_POSITIVE 279 92 58 137 100 NC_009009:SSA_0577|5end_Ancient_RNA-binding_IF3-C_fold_(CRS1/YhbY_domain),_putative_571253..571483_POSITIVE 278 165 132 82 50 NC_009009:SSA_1536|5end_Biotin_synthase,_putative_1543609..1543839_POSITIVE 278 86 50 192 140 NC_009009:SSA_1012|5end_Phosphoenolpyruvate_synthase,_putative_1014739..1014969_POSITIVE 277 116 71 79 27 NC_009009:SSA_0350|5end_Helicase,_putative_344218..344448_NEGATIVE 276 96 51 210 156 NC_009009:SSA_1379|5end_hypothetical_protein_1398528..1398758_NEGATIVE 275 166 135 185 152 NC_009009:SSA_0415|5end_Permease,_putative_410568..410798_POSITIVE 272 220 190 231 190 NC_009009:SSA_0410|5end_hypothetical_protein_406442..406672_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 291 162 130 59 18 NC_009009:SSA_2168|3end_Glycerol-3-phosphate_dehydrogenase_[NAD(P)+],_putative_2168563..2168713_POSITIVE 285 85 51 110 79 NC_009009:SSA_0272|3end_Oxidoreductase,_aldo/keto_reductase_family,_putative_267032..267182_POSITIVE 285 161 130 69 39 NC_009009:SSA_0070|3end_Acetylxylan_esterase,_putative_74914..75064_POSITIVE 282 180 145 37 1 NC_009009:SSA_1679|3end_ABC-type_multidrug_transport_system,_ATPase_component,_putative_1672183..1672333_NEGATIVE 280 165 121 102 48 NC_009009:SSA_1048|3end_ABC_transporter_ATP-binding_protein-spermidine/putrescine_transport,_putative_1064184..1064334_POSITIVE 275 166 135 106 73 NC_009009:SSA_0414|3end_hypothetical_protein_410569..410719_POSITIVE 268 87 52 56 9 NC_009009:SSA_1043|3end_Homoserine_dehydrogenase,_putative_1059931..1060081_POSITIVE 268 90 50 85 33 NC_009009:SSA_1015|3end_4-hydroxybenzoate_octaprenyltransferase,_putative_1019682..1019832_POSITIVE 266 179 135 99 52 NC_009009:SSA_1014|3end_Phosphatidylserine_decarboxylase_proenzyme_2,_putative_1018798..1018948_POSITIVE 262 88 50 92 49 NC_009009:SSA_0083|3end_hypothetical_protein_85840..85990_POSITIVE 261 91 51 36 7 NC_009009:SSA_0375|3end_D-methionine-binding_lipoprotein_(ABC-type_transporter),_putative_365209..365359_POSITIVE 261 165 139 146 119 NC_009009:SSA_0306|3end_Transcription_regulator_(glutamine_synthetase_repressor),_putative_303035..303185_POSITIVE 260 86 50 133 101 NC_009009:SSA_1741|3end_ABC-type_Fe3+-siderophores_transporter,_ATPase_component,_putative_1728872..1729022_POSITIVE 259 86 43 131 96 NC_009009:SSA_0341|3end_hypothetical_protein_333955..334105_NEGATIVE 258 159 131 151 116 NC_009009:SSA_0745|3end_hypothetical_protein_726814..726964_NEGATIVE 256 102 61 141 100 NC_009009:SSA_1344|3end_Xanthine/uracil_permeases,_putative_1362069..1362219_NEGATIVE 254 93 58 40 12 NC_009009:SSA_0510|3end_L-threonine-O-3-phosphate_decarboxylase,_putative_509697..509847_POSITIVE 250 180 135 151 104 NC_009009:SSA_2211|3end_Transmembrane_protein,_putative_2211499..2211649_NEGATIVE 250 170 122 141 95 NC_009009:SSA_1398|3end_Membrane_protein,_hemolysin_III-like,_putative_1411626..1411776_POSITIVE 250 91 52 90 45 NC_009009:SSA_0497|3end_Nickel_ABC_transporter,_putative_497997..498147_POSITIVE