Origin IGS: tttaaaggaggaaataaattatgggacttttaaaagacataaaagaattggttggtattaatactggtgatgatgaggaagatatagaagaaatggaacaagaacaaacttcaaaagcactttcaaaaaggcaaaaa .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tttttgcctttttgaaagtgcttttgaagtttgttcttgttccatttcttctatatcttcctcatcatcaccagtattaataccaaccaattcttttatgtcttttaaaagtcccataatttatttcctcctttaaa Mask Tandem Repeat Region ================================================ tttaaaggaggaaataaattatgggacttttaaaagacataaaagaattggttggtattaatactggtgatgatgaggaagatatagaagaaatggaacaagaacaaacttcaaaagcactttcaaaaaggcaaaaa Find is-nt database================================================ Query_seq: FN0561:FN0562|FN0561:FN0562:Proline synthetase associated protein:Hypothetical cytosolic protein:->->:1214967..1215103 137 tttaaaggaggaaataaattatgggacttttaaaagacataaaagaattggttggtattaatactggtgatgatgaggaagatatagaagaaatggaacaagaacaaacttcaaaagcactttcaaaaaggcaaaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN0561:FN0562|FN0561:FN0562:Proline synthetase associated protein:Hypothetical cytosolic protein:->->:1214967..1215103 137 tttaaaggaggaaataaattatgggacttttaaaagacataaaagaattggttggtattaatactggtgatgatgaggaagatatagaagaaatggaacaagaacaaacttcaaaagcactttcaaaaaggcaaaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN0561:FN0562|FN0561:FN0562:Proline synthetase associated protein:Hypothetical cytosolic protein:->->:1214967..1215103 137 tttaaaggaggaaataaattatgggacttttaaaagacataaaagaattggttggtattaatactggtgatgatgaggaagatatagaagaaatggaacaagaacaaacttcaaaagcactttcaaaaaggcaaaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tttaaaggaggaaataaattatgggacttttaaaagacataaaagaattggttggtattaatactggtgatgatgaggaagatatagaagaaatggaacaagaacaaacttcaaaagcactttcaaaaaggcaaaaa Predict ORF larger than 30AA ================================================ Protein_Len: 40 Strand: + Start: 18 End: 137 ................. M M G L L K D I K E L V G I N T G D D E E D I E E M E Q E Q T S K A L S K R Q K Protein_Len: 31 Strand: - Start: 5 End: 94 .... * L L F Y I I P S K F S M F S N T P I L V P S S S S S I S S M ........................................... tttaaaggaggaaataaattatgggacttttaaaagacataaaagaattggttggtattaatactggtgatgatgaggaagatatagaagaaatggaacaagaacaaacttcaaaagcactttcaaaaaggcaaaaa 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================================================ tttaaaggaggaaataaattatgggacttttaaaagacataaaagaattggttggtattaatactggtgatgatgaggaagatatagaagaaatggaacaagaacaaacttcaaaagcactttcaaaaaggcaaaaa Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: FN0561:FN0562|FN0561:FN0562:Proline synthetase associated protein:Hypothetical cytosolic protein:->->:1214967..1215103 137 tttaaaggaggaaataaattatgggacttttaaaagacataaaagaattggttggtattaatactggtgatgatgaggaagatatagaagaaatggaacaagaacaaacttcaaaagcactttcaaaaaggcaaaaa Intra-Species Hit: Count: 1 Min: 1 Max: 137 Len: 137 Subject: NC_003454_FN0561_FN0562|Proline synthetase associated protein:Hypothetical cytosolic protein|POSITIVE:POSITIVE|[1214967,1215103]|137 HSP 1 e-value: 3.0E-72 bit: 272.0 Len: 137 Query Start:1 Query End:137 Subject Strand: POSITIVE Subject Start: 1 Subject End: 137 tttaaaggaggaaataaattatgggacttttaaaagacataaaagaattggttggtattaatactggtgatgatgaggaagatatagaagaaatggaacaagaacaaacttcaaaagcactttcaaaaaggcaaaaa tttaaaggaggaaataaattatgggacttttaaaagacataaaagaattggttggtattaatactggtgatgatgaggaagatatagaagaaatggaacaagaacaaacttcaaaagcactttcaaaaaggcaaaaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUAAAGGAGGAAAUAAAUUAUGGGACUUUUAAAAGACAUAAAAGAAUUGGUUGGUAUUAAUACUGGUGAUGAUGAGGAAGAUAUAGAAGAAAUGGAACAAGAACAAACUUCAAAAGCACUUUCAAAAAGGCAAAAA ......(((((......(((((.((.((((((.......)))))).((((((....)))))).)).)))))...............((((...((.........))..)))).......)))))............. (-13.00) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUUUGCCUUUUUGAAAGUGCUUUUGAAGUUUGUUCUUGUUCCAUUUCUUCUAUAUCUUCCUCAUCAUCACCAGUAUUAAUACCAACCAAUUCUUUUAUGUCUUUUAAAAGUCCCAUAAUUUAUUUCCUCCUUUAAA ........((((((((((.((....((((..((.........))...))))......................(((....)))................)))))))))))).......................... ( -7.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 279 89 47 181 137 NC_003454:FN0797|5end_hypothetical_protein_1455799..1456029_NEGATIVE 272 49 6 209 165 NC_003454:FN0711|5end_Phosphopantothenate--cysteine_ligase_1369569..1369799_POSITIVE 209 106 61 134 86 NC_003454:FN0246|5end_hypothetical_protein_870797..871027_NEGATIVE 193 110 66 56 12 NC_003454:FN0115|5end_hypothetical_protein_748511..748741_NEGATIVE 192 98 54 69 28 NC_003454:FN0112|5end_hypothetical_protein_746353..746583_POSITIVE 185 107 63 114 69 NC_003454:FN0601|5end_Hypothetical_exported_24-amino_acid_repeat_protein_1256527..1256757_NEGATIVE 175 100 53 221 176 NC_003454:FN1974|5end_DNA/RNA_helicase_(DEAD/DEAH_BOX_family)_475526..475756_NEGATIVE 172 119 75 86 45 NC_003454:FN1251|5end_High-affinity_iron_permease_1908008..1908238_POSITIVE 171 121 88 47 20 NC_003454:FN0367|5end_Integral_membrane_protein_996901..997131_NEGATIVE 171 126 107 60 36 NC_003454:FN1703|5end_ADP-L-glycero-D-manno-heptose-6-epimerase_198992..199222_NEGATIVE 170 103 73 209 183 NC_003454:FN1462|5end_Transcriptional_regulator,_GntR_family_2144945..2145175_NEGATIVE 170 89 64 53 25 NC_003454:FN0914|5end_hypothetical_protein_1571528..1571758_NEGATIVE 169 26 6 211 194 NC_003454:FN1418|5end_AMINOTRANSFERASE_CLASS-I_2080500..2080730_NEGATIVE 169 98 62 182 142 NC_003454:FN0222|5end_Melibiose_carrier_protein_846812..847042_POSITIVE 168 87 47 160 120 NC_003454:FN0974|5end_Lactoylglutathione_lyase_1627144..1627374_NEGATIVE 166 34 6 223 195 NC_003454:FN1129|5end_Chromosome_partition_protein_smc_1774204..1774434_POSITIVE 166 114 71 69 27 NC_003454:FN0947|5end_hypothetical_protein_1600457..1600687_POSITIVE 163 119 78 69 24 NC_003454:FN1938|5end_hypothetical_protein_438416..438646_NEGATIVE 162 96 64 97 67 NC_003454:FN0665|5end_N-acetylmuramoyl-L-alanine_amidase_1321085..1321315_POSITIVE 162 100 64 107 73 NC_003454:FN0049|5end_hypothetical_protein_686351..686581_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 263 97 62 47 13 NC_003454:FN1288|3end_hypothetical_protein_1944830..1944980_POSITIVE 237 104 61 86 46 NC_003454:FN1018|3end_hypothetical_protein_1672145..1672295_NEGATIVE 198 90 41 54 5 NC_003454:FN1194|3end_hypothetical_protein_1855668..1855818_POSITIVE 197 96 51 55 13 NC_003454:FN0332|3end_Magnesium_and_cobalt_transport_protein_corA_966175..966325_NEGATIVE 189 100 52 97 58 NC_003454:FN1467|3end_hypothetical_protein_2149841..2149991_POSITIVE 189 98 65 68 31 NC_003454:FN0115|3end_hypothetical_protein_748215..748365_NEGATIVE 185 73 43 89 59 NC_003454:FN1732|3end_hypothetical_protein_231281..231431_NEGATIVE 183 80 48 52 20 NC_003454:FN0123|3end_ATPase_755027..755177_POSITIVE 175 104 72 38 6 NC_003454:FN0219|3end_Autolysin_response_regulator_842594..842744_NEGATIVE 174 94 53 102 65 NC_003454:FN0935|3end_hypothetical_protein_1587558..1587708_NEGATIVE 170 89 64 38 10 NC_003454:FN0915|3end_PTS_system,_N-acetylglucosamine-specific_IIA_component_1571543..1571693_NEGATIVE 167 69 21 100 48 NC_003454:FN1019|3end_3-hydroxybutyryl-CoA_dehydrogenase_1672945..1673095_NEGATIVE 165 93 53 125 75 NC_003454:FN1344|3end_hypothetical_protein_1998034..1998184_POSITIVE 165 76 47 147 118 NC_003454:FN1646|3end_SSU_ribosomal_protein_S10P_141449..141599_NEGATIVE 163 67 25 78 38 NC_003454:FN1705|3end_hypothetical_protein_201464..201614_NEGATIVE 160 86 54 132 98 NC_003454:FN0799|3end_Isoamylase_1457889..1458039_NEGATIVE 160 126 86 47 1 NC_003454:FN0235|3end_ABC_transporter_ATP-binding_protein_859674..859824_NEGATIVE 159 80 35 53 7 NC_003454:FN0316|3end_hypothetical_protein_953234..953384_NEGATIVE 157 48 6 65 17 NC_003454:FN0480|3end_hypothetical_protein_1127839..1127989_POSITIVE 156 48 6 48 8 NC_003454:FN1674|3end_hypothetical_protein_172225..172375_POSITIVE