Origin IGS: taaatgtaaagaaactgagacataatgtcttggtttttttatattcgtatgaatttttaaacactttgaataaaaatgttgataaattgcaatactcttggtataataagctacgaaaggagtataag .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 cttatactcctttcgtagcttattataccaagagtattgcaatttatcaacatttttattcaaagtgtttaaaaattcatacgaatataaaaaaaccaagacattatgtctcagtttctttacattta Mask Tandem Repeat Region ================================================ taaatgtaaagaaactgagacataatgtcttggtttttttatattcgtatgaatttttaaacactttgaataaaaatgttgataaattgcaatactcttggtataataagctacgaaaggagtataag Find is-nt database================================================ Query_seq: SSA_0804:SSA_0805|SSA_0804:SSA_0805:Phosphoglucomutase/phosphomannomutase family protein, putative:Collagen-binding surface protein, putative:->->:787488..787615 128 taaatgtaaagaaactgagacataatgtcttggtttttttatattcgtatgaatttttaaacactttgaataaaaatgttgataaattgcaatactcttggtataataagctacgaaaggagtataag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0804:SSA_0805|SSA_0804:SSA_0805:Phosphoglucomutase/phosphomannomutase family protein, putative:Collagen-binding surface protein, putative:->->:787488..787615 128 taaatgtaaagaaactgagacataatgtcttggtttttttatattcgtatgaatttttaaacactttgaataaaaatgttgataaattgcaatactcttggtataataagctacgaaaggagtataag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0804:SSA_0805|SSA_0804:SSA_0805:Phosphoglucomutase/phosphomannomutase family protein, putative:Collagen-binding surface protein, putative:->->:787488..787615 128 taaatgtaaagaaactgagacataatgtcttggtttttttatattcgtatgaatttttaaacactttgaataaaaatgttgataaattgcaatactcttggtataataagctacgaaaggagtataag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taaatgtaaagaaactgagacataatgtcttggtttttttatattcgtatgaatttttaaacactttgaataaaaatgttgataaattgcaatactcttggtataataagctacgaaaggagtataag Predict ORF larger than 30AA ================================================ Protein_Len: 38 Strand: + Start: 15 End: 128 .............. M R H N V L V F L Y S Y E F L N T L N K N V D K L Q Y S W Y N K L R K E Y K Protein_Len: 31 Strand: - Start: 1 End: 93 L H L S V S V Y H R P K K I N T H I K L C K S Y F H Q Y I A M ................................... taaatgtaaagaaactgagacataatgtcttggtttttttatattcgtatgaatttttaaacactttgaataaaaatgttgataaattgcaatactcttggtataataagctacgaaaggagtataag 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: 92 Start: 78 End: 107 .............................................................................GTTGATAAATTGCAATACTCTTGGTATAAT..................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ taaatgtaaagaaactgagacataatgtcttggtttttttatattcgtatgaatttttaaacactttgaataaaaatgttgataaattgcaatactcttggtataataagctacgaaaggagtataag Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_0804:SSA_0805|SSA_0804:SSA_0805:Phosphoglucomutase/phosphomannomutase family protein, putative:Collagen-binding surface protein, putative:->->:787488..787615 128 taaatgtaaagaaactgagacataatgtcttggtttttttatattcgtatgaatttttaaacactttgaataaaaatgttgataaattgcaatactcttggtataataagctacgaaaggagtataag Intra-Species Hit: Count: 1 Min: 1 Max: 128 Len: 128 Subject: NC_009009_SSA_0804_SSA_0805|Phosphoglucomutase/phosphomannomutase family protein, putative:Collagen-binding surface protein, putative|POSITIVE:POSITIVE|[787488,787615]|128 HSP 1 e-value: 2.0E-54 bit: 212.0 Len: 128 Query Start:1 Query End:128 Subject Strand: POSITIVE Subject Start: 1 Subject End: 128 taaatgtaaagaaactgagacataatgtcttggnnnnnnnatattcgtatgaatttttaaacactttgaataaaaatgttgataaattgcaatactcttggtataataagctacgaaaggagtataag taaatgtaaagaaactgagacataatgtcttggtttttttatattcgtatgaatttttaaacactttgaataaaaatgttgataaattgcaatactcttggtataataagctacgaaaggagtataag Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAAUGUAAAGAAACUGAGACAUAAUGUCUUGGUUUUUUUAUAUUCGUAUGAAUUUUUAAACACUUUGAAUAAAAAUGUUGAUAAAUUGCAAUACUCUUGGUAUAAUAAGCUACGAAAGGAGUAUAAG ..(((((((((((((..((((.....))))..)))))))))))))......(((((...((((.(((.....))).))))...)))))...((((((((.(((........)))...))))))))... (-31.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUUAUACUCCUUUCGUAGCUUAUUAUACCAAGAGUAUUGCAAUUUAUCAACAUUUUUAUUCAAAGUGUUUAAAAAUUCAUACGAAUAUAAAAAAACCAAGACAUUAUGUCUCAGUUUCUUUACAUUUA ...((((((.....(((........)))...))))))((.(((((.(.((((((((.....)))))))).).)))))))...((((.((((.((((..((((.....))))..)))).)))).)))). (-18.10) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 246 50 4 225 176 NC_009009:SSA_1949|5end_AliA_protein,_putative_1944373..1944603_NEGATIVE 235 48 8 209 157 NC_009009:SSA_0790|5end_hypothetical_protein_773047..773277_POSITIVE 218 51 13 68 30 NC_009009:SSA_2094|5end_Conserved_uncharacterized_protein_2098247..2098477_NEGATIVE 213 48 14 68 35 NC_009009:SSA_1612|5end_Diacylglycerol_kinase,_putative_1616497..1616727_NEGATIVE 212 38 6 225 193 NC_009009:SSA_0150|5end_hypothetical_protein_143936..144166_POSITIVE 202 120 86 47 5 NC_009009:SSA_1277|5end_D-alanyl-D-alanine_carboxypeptidase_1299216..1299446_NEGATIVE 202 44 3 207 171 NC_009009:SSA_0655|5end_Cell_division_protein_FtsA,_putative_638784..639014_POSITIVE 195 68 30 105 75 NC_009009:SSA_0498|5end_ABC-type_dipeptide/oligopeptide/nickel_transport_systems,_permease_components,_putative_497910..498140_POSITIVE 189 56 15 207 164 NC_009009:SSA_2233|5end_hypothetical_protein_2233110..2233340_NEGATIVE 189 48 2 163 112 NC_009009:SSA_1473|5end_hypothetical_protein_1478920..1479150_NEGATIVE 185 70 21 135 89 NC_009009:SSA_0264|5end_PEP_phosphonomutase-like_protein,_putative_258400..258630_POSITIVE 184 90 44 124 75 NC_009009:SSA_0482|5end_ATP:cobalamin_adenosyl_transferase,_putative_483458..483688_POSITIVE 183 106 63 219 172 NC_009009:SSA_2327|5end_hypothetical_protein_2330925..2331155_POSITIVE 183 55 15 44 2 NC_009009:SSA_1294|5end_hypothetical_protein_1312581..1312811_NEGATIVE 180 60 16 40 1 NC_009009:SSA_2189|5end_hypothetical_protein_2191097..2191327_NEGATIVE 180 47 6 188 146 NC_009009:SSA_1861|5end_Aminopeptidase_C,_putative_1857902..1858132_NEGATIVE 179 114 75 98 57 NC_009009:SSA_0449|5end_Aminopeptidase_P;_XAA-pro_aminopeptidase,_putative_449464..449694_POSITIVE 177 111 77 73 41 NC_009009:SSA_1866|5end_hypothetical_protein_1862182..1862412_NEGATIVE 177 38 8 140 106 NC_009009:SSA_1490|5end_Ribonuclease_BN,_putative_1496732..1496962_NEGATIVE 177 115 77 184 147 NC_009009:SSA_0913|5end_Acetyltransferase,_putative_924195..924425_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 363 45 3 88 46 NC_009009:SSA_0804|3end_Phosphoglucomutase/phosphomannomutase_family_protein,_putative_787427..787577_POSITIVE 319 45 8 82 43 NC_009009:SSA_1909|3end_Transcriptional_attenuator_LytR,_putative_1900904..1901054_NEGATIVE 277 45 3 57 9 NC_009009:SSA_1543|3end_hypothetical_protein_1548217..1548367_POSITIVE 263 49 6 60 13 NC_009009:SSA_0648|3end_hypothetical_protein_631775..631925_POSITIVE 261 48 10 45 6 NC_009009:SSA_1544|3end_Conserved_uncharacterized_protein_1548314..1548464_NEGATIVE 249 38 5 92 58 NC_009009:SSA_0267|3end_ROK_family_protein,_putative_260873..261023_NEGATIVE 242 40 5 38 6 NC_009009:SSA_0266|3end_ORFB,_transposon_ISSsa1_260822..260972_POSITIVE 222 40 6 77 44 NC_009009:SSA_2265|3end_Maltodextrin_phosphorylase,_putative_2261936..2262086_NEGATIVE 220 49 5 100 54 NC_009009:SSA_0395|3end_6-phospho-beta-glucosidase,_putative_392580..392730_POSITIVE 213 48 14 87 54 NC_009009:SSA_1613|3end_hypothetical_protein_1616478..1616628_NEGATIVE 212 38 6 42 10 NC_009009:SSA_0149|3end_hypothetical_protein_143833..143983_POSITIVE 205 40 2 81 38 NC_009009:SSA_1205|3end_Bta,_putative_1230057..1230207_POSITIVE 204 40 3 90 50 NC_009009:SSA_0649|3end_Ribosomal_small_subunit_pseudouridine_synthase_A,_putative_631820..631970_NEGATIVE 202 44 3 85 49 NC_009009:SSA_0654|3end_Cell_division_protein_DivIB,_putative_638742..638892_POSITIVE 195 68 30 112 82 NC_009009:SSA_0497|3end_Nickel_ABC_transporter,_putative_497997..498147_POSITIVE 194 59 28 107 74 NC_009009:SSA_1625|3end_Lactoylglutathione_lyase,_putative_1626577..1626727_NEGATIVE 190 40 9 79 48 NC_009009:SSA_1591|3end_Dipeptidase,_putative_1593403..1593553_NEGATIVE 189 56 15 76 33 NC_009009:SSA_2234|3end_Phosphatidylserine/phosphatidylglycerophosphate/_cardiolipin_synthase,_phospholipase_D_family,_putative_2233241..2233391_NEGATIVE 188 48 8 98 58 NC_009009:SSA_1206|3end_A/G-specific_adenine_glycosylase,_putative_1230071..1230221_NEGATIVE 186 41 9 93 63 NC_009009:SSA_2301|3end_S-layer_protein/_peptidoglycan_endo-beta-N-acetylglucosaminidase,_putative_2302669..2302819_NEGATIVE