Origin IGS: ggataatatctcctaattttctcttttgatattgccaaaatagttgtcatcatctgacaactactttggtaatatccgactgccatggcagtcggaatagagattttctctaattttctatta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 taatagaaaattagagaaaatctctattccgactgccatggcagtcggatattaccaaagtagttgtcagatgatgacaactattttggcaatatcaaaagagaaaattaggagatattatcc Mask Tandem Repeat Region ================================================ ggataatatctcctaattttctcttttgatattgccaaaatagttgtcatcatctgacaactactttggtaatatccgactgccatggcagtcggaatagagattttctctaattttctatta Find is-nt database================================================ Query_seq: SSA_2312:SSA_2313|SSA_2312:SSA_2313:hypothetical protein:hypothetical protein:<-<-:2315372..2315494 123 ggataatatctcctaattttctcttttgatattgccaaaatagttgtcatcatctgacaactactttggtaatatccgactgccatggcagtcggaatagagattttctctaattttctatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_2312:SSA_2313|SSA_2312:SSA_2313:hypothetical protein:hypothetical protein:<-<-:2315372..2315494 123 ggataatatctcctaattttctcttttgatattgccaaaatagttgtcatcatctgacaactactttggtaatatccgactgccatggcagtcggaatagagattttctctaattttctatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_2312:SSA_2313|SSA_2312:SSA_2313:hypothetical protein:hypothetical protein:<-<-:2315372..2315494 123 ggataatatctcctaattttctcttttgatattgccaaaatagttgtcatcatctgacaactactttggtaatatccgactgccatggcagtcggaatagagattttctctaattttctatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ggataatatctcctaattttctcttttgatattgccaaaatagttgtcatcatctgacaactactttggtaatatccgactgccatggcagtcggaatagagattttctctaattttctatta Predict ORF larger than 30AA ================================================ Protein_Len: 34 Strand: - Start: 3 End: 104 .. Y Y R R I K E K S I A L I T T M M Q C S S Q Y Y G V A M A T P I S M ................... ggataatatctcctaattttctcttttgatattgccaaaatagttgtcatcatctgacaactactttggtaatatccgactgccatggcagtcggaatagagattttctctaattttctatta 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================================================ ggataatatctcctaattttctcttttgatattgccaaaatagttgtcatcatctgacaactactttggtaatatccgactgccatggcagtcggaatagagattttctctaattttctatta Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 88 HP_score: -13.1 Tail_Score: -2.62983 Start: 35 End: 69 Full_Region: TCTCTTTTGATATTG CCAAAATAGTTGTCA TCATC TGACAACTACTTTGG TAATATCCGACTGCC ..................................CCAAAATAGTTGTCATCATCTGACAACTACTTTGG...................................................... TransTerm Strand: + Conf: 63 HP_score: -5.8 Tail_Score: -3.81951 Start: 40 End: 64 Full_Region: TTTGATATTGCCAAA ATAGTTGTCA TCATC TGACAACTAC TTTGGTAATATCCGA .......................................ATAGTTGTCATCATCTGACAACTAC........................................................... TransTerm Strand: + Conf: 73 HP_score: -9.3 Tail_Score: -2.88849 Start: 41 End: 63 Full_Region: TTGATATTGCCAAAA TAGTTGTCA TCATC TGACAACTA CTTTGGTAATATCCG ........................................TAGTTGTCATCATCTGACAACTA............................................................ TransTerm Strand: - Conf: 85 HP_score: -9.3 Tail_Score: -4.13014 Start: 41 End: 63 Full_Region: cggatattaccaaag tagttgtca gatga tgacaacta ttttggcaatatcaa ........................................tagttgtcagatgatgacaacta............................................................ Find igs database================================================ Query_seq: SSA_2312:SSA_2313|SSA_2312:SSA_2313:hypothetical protein:hypothetical protein:<-<-:2315372..2315494 123 ggataatatctcctaattttctcttttgatattgccaaaatagttgtcatcatctgacaactactttggtaatatccgactgccatggcagtcggaatagagattttctctaattttctatta Intra-Species Hit: Count: 1 Min: 1 Max: 123 Len: 123 Subject: NC_009009_SSA_2312_SSA_2313|hypothetical protein:hypothetical protein|NEGATIVE:NEGATIVE|[2315372,2315494]|123 HSP 1 e-value: 6.0E-64 bit: 244.0 Len: 123 Query Start:1 Query End:123 Subject Strand: POSITIVE Subject Start: 1 Subject End: 123 ggataatatctcctaattttctcttttgatattgccaaaatagttgtcatcatctgacaactactttggtaatatccgactgccatggcagtcggaatagagattttctctaattttctatta ggataatatctcctaattttctcttttgatattgccaaaatagttgtcatcatctgacaactactttggtaatatccgactgccatggcagtcggaatagagattttctctaattttctatta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GGAUAAUAUCUCCUAAUUUUCUCUUUUGAUAUUGCCAAAAUAGUUGUCAUCAUCUGACAACUACUUUGGUAAUAUCCGACUGCCAUGGCAGUCGGAAUAGAGAUUUUCUCUAAUUUUCUAUUA (((.((.(((((.................((((((((((.(((((((((.....))))))))).))))))))))(((((((((....)))))))))...))))).)).)))............ (-46.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAUAGAAAAUUAGAGAAAAUCUCUAUUCCGACUGCCAUGGCAGUCGGAUAUUACCAAAGUAGUUGUCAGAUGAUGACAACUAUUUUGGCAAUAUCAAAAGAGAAAAUUAGGAGAUAUUAUCC .............((.((.((((((....(((((((....)))))))((((((.(((((((((((((((.....))))))))))))))).))))))..............)))))).)).)). (-46.50) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 945 100 51 191 142 NC_009009:SSA_2312|5end_hypothetical_protein_2315281..2315511_NEGATIVE 314 88 41 198 142 NC_009009:SSA_0940|5end_NOL1/NOP2/sun_family_protein,_putative_947626..947856_POSITIVE 300 96 52 101 48 NC_009009:SSA_0188|5end_hypothetical_protein_190798..191028_POSITIVE 293 98 53 139 84 NC_009009:SSA_1872|5end_Cell_division_protein,_putative_1869186..1869416_NEGATIVE 288 102 64 204 154 NC_009009:SSA_2194|5end_Nicotinamide_mononucleotide_transporter,_putative_2195663..2195893_NEGATIVE 285 103 61 63 19 NC_009009:SSA_0588|5end_L-cystine_ABC_transporter,_substrate-binding_component,_putative_579800..580030_POSITIVE 282 90 43 226 162 NC_009009:SSA_1307|5end_Trk_transporter_membrane-spanning_protein-K+_transport,_putative_1326270..1326500_NEGATIVE 281 119 75 62 5 NC_009009:SSA_1854|5end_Conserved_uncharacterized_protein_1850884..1851114_NEGATIVE 279 95 52 58 5 NC_009009:SSA_0219|5end_PTS_system,_sugar-specific_enzyme_IIA_component,_putative_215367..215597_POSITIVE 278 109 77 208 171 NC_009009:SSA_1760|5end_hypothetical_protein_1747284..1747514_NEGATIVE 277 109 64 171 119 NC_009009:SSA_1592|5end_hypothetical_protein_1596397..1596627_NEGATIVE 272 58 13 138 95 NC_009009:SSA_2072|5end_Phosphatidate_cytidylyltransferase,_putative_2075603..2075833_NEGATIVE 270 94 52 104 50 NC_009009:SSA_1606|5end_Dephospho-CoA_kinase,_putative_1612425..1612655_NEGATIVE 266 90 46 62 17 NC_009009:SSA_0489|5end_Adenosylcobinamide_kinase_/_adenosylcobinamide_phosphate_guanyltransferase,_putative_489655..489885_POSITIVE 265 111 72 113 75 NC_009009:SSA_0706|5end_RNA_helicase,_putative_691363..691593_POSITIVE 264 97 53 71 30 NC_009009:SSA_0037|5end_Phosphoribosylamine-glycine_ligase;_phosphoribosyl_glycinamide_synthetase_(GARS),_putative_44272..44502_POSITIVE 263 109 66 225 164 NC_009009:SSA_2169|5end_Glucose-1-phosphate_uridylyltransferase,_putative_2168446..2168676_POSITIVE 261 109 68 78 38 NC_009009:SSA_0626|5end_hypothetical_protein_616089..616319_POSITIVE 259 110 76 43 1 NC_009009:SSA_0241|5end_Ribosomal_protein_L11_methyltransferase,_putative_234021..234251_POSITIVE 257 111 76 83 40 NC_009009:SSA_2142|5end_Argininosuccinate_synthase,_putative_2143415..2143645_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 300 96 52 75 22 NC_009009:SSA_0187|3end_Competence_protein_ComYD,_putative_190852..191002_POSITIVE 293 98 53 131 76 NC_009009:SSA_1873|3end_S-adenosyl-methyltransferase_mraW,_putative_1869194..1869344_NEGATIVE 278 109 77 55 18 NC_009009:SSA_1761|3end_Hemolysin_(containing_CBS_domains),_putative_1747437..1747587_NEGATIVE 275 117 74 106 61 NC_009009:SSA_0368|3end_hypothetical_protein_359722..359872_POSITIVE 272 58 13 119 76 NC_009009:SSA_2073|3end_Undecaprenyl_pyrophosphate_synthetase,_putative_2075622..2075772_NEGATIVE 270 94 52 98 44 NC_009009:SSA_1607|3end_Formamidopyrimidine-DNA_glycosylase,_putative_1612431..1612581_NEGATIVE 266 90 46 69 24 NC_009009:SSA_0488|3end_Glutamate-1-semialdehyde_2,1-aminotransferase,_putative_489742..489892_POSITIVE 261 109 68 91 51 NC_009009:SSA_0625|3end_Phosphopantetheine_adenylyltransferase_616182..616332_POSITIVE 256 60 13 61 20 NC_009009:SSA_0677|3end_rRNA_methylase,_putative_660361..660511_POSITIVE 256 99 64 45 7 NC_009009:SSA_0103|3end_Integral_membrane_protein,_putative_104630..104780_NEGATIVE 252 95 58 141 103 NC_009009:SSA_0017|3end_Cell_shape_determining_protein_MreC,_putative_23706..23856_POSITIVE 250 55 11 118 64 NC_009009:SSA_1549|3end_hypothetical_protein_1551816..1551966_NEGATIVE 249 105 68 66 23 NC_009009:SSA_0489|3end_Adenosylcobinamide_kinase_/_adenosylcobinamide_phosphate_guanyltransferase,_putative_490319..490469_POSITIVE 246 90 41 130 75 NC_009009:SSA_1429|3end_hypothetical_protein_1436355..1436505_NEGATIVE 241 58 16 136 87 NC_009009:SSA_1254|3end_hypothetical_protein_1281242..1281392_NEGATIVE 238 58 18 110 64 NC_009009:SSA_0306|3end_Transcription_regulator_(glutamine_synthetase_repressor),_putative_303035..303185_POSITIVE 237 100 52 131 83 NC_009009:SSA_0756|3end_Alanyl-tRNA_synthetase,_putative_739434..739584_POSITIVE 236 99 56 127 69 NC_009009:SSA_1491|3end_Methionine_aminopeptidase_A,_putative_1496780..1496930_NEGATIVE 236 110 66 146 110 NC_009009:SSA_1416|3end_hypothetical_protein_1426520..1426670_NEGATIVE 236 108 80 147 123 NC_009009:SSA_1079|3end_hypothetical_protein_1097448..1097598_POSITIVE