Origin IGS: aaacttcctccagttttcattaagattactttcattatagcacttctgtgacaggatgtaaacgcttcaatgcaatagagagtcatataaaaaaagagactgggacaaaatgtctcagtctcgctttatcgtattcacaaacttttgattccaaactgtttataaagaatcaaaaattcgcggttcagaacc .........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 ggttctgaaccgcgaatttttgattctttataaacagtttggaatcaaaagtttgtgaatacgataaagcgagactgagacattttgtcccagtctctttttttatatgactctctattgcattgaagcgtttacatcctgtcacagaagtgctataatgaaagtaatcttaatgaaaactggaggaagttt Mask Tandem Repeat Region ================================================ aaacttcctccagttttcattaagattactttcattatagcacttctgtgacaggatgtaaacgcttcaatgcaatagagagtcatataaaaaaagagactgggacaaaatgtctcagtctcgctttatcgtattcacaaacttttgattccaaactgtttataaagaatcaaaaattcgcggttcagaacc Find is-nt database================================================ Query_seq: SSA_1949:SSA_1950|SSA_1949:SSA_1950:AliA protein, putative:ABC-type oligopeptide transport system, periplasmic component, putative:<-<-:1944464..1944655 192 aaacttcctccagttttcattaagattactttcattatagcacttctgtgacaggatgtaaacgcttcaatgcaatagagagtcatataaaaaaagagactgggacaaaatgtctcagtctcgctttatcgtattcacaaacttttgattccaaactgtttataaagaatcaaaaattcgcggttcagaacc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1949:SSA_1950|SSA_1949:SSA_1950:AliA protein, putative:ABC-type oligopeptide transport system, periplasmic component, putative:<-<-:1944464..1944655 192 aaacttcctccagttttcattaagattactttcattatagcacttctgtgacaggatgtaaacgcttcaatgcaatagagagtcatataaaaaaagagactgggacaaaatgtctcagtctcgctttatcgtattcacaaacttttgattccaaactgtttataaagaatcaaaaattcgcggttcagaacc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1949:SSA_1950|SSA_1949:SSA_1950:AliA protein, putative:ABC-type oligopeptide transport system, periplasmic component, putative:<-<-:1944464..1944655 192 aaacttcctccagttttcattaagattactttcattatagcacttctgtgacaggatgtaaacgcttcaatgcaatagagagtcatataaaaaaagagactgggacaaaatgtctcagtctcgctttatcgtattcacaaacttttgattccaaactgtttataaagaatcaaaaattcgcggttcagaacc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aaacttcctccagttttcattaagattactttcattatagcacttctgtgacaggatgtaaacgcttcaatgcaatagagagtcatataaaaaaagagactgggacaaaatgtctcagtctcgctttatcgtattcacaaacttttgattccaaactgtttataaagaatcaaaaattcgcggttcagaacc Predict ORF larger than 30AA ================================================ Protein_Len: 48 Strand: + Start: 48 End: 191 ............................................... M T G C K R F N A I E S H I K K E T G T K C L S L A L S Y S Q T F D S K L F I K N Q K F A V Q N . aaacttcctccagttttcattaagattactttcattatagcacttctgtgacaggatgtaaacgcttcaatgcaatagagagtcatataaaaaaagagactgggacaaaatgtctcagtctcgctttatcgtattcacaaacttttgattccaaactgtttataaagaatcaaaaattcgcggttcagaacc 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: 87 Start: 34 End: 63 .................................GTTTACATCCTGTCACAGAAGTGCTATAAT................................................................................................................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aaacttcctccagttttcattaagattactttcattatagcacttctgtgacaggatgtaaacgcttcaatgcaatagagagtcatataaaaaaagagactgggacaaaatgtctcagtctcgctttatcgtattcacaaacttttgattccaaactgtttataaagaatcaaaaattcgcggttcagaacc Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 82 HP_score: -9.0 Tail_Score: -4.06384 Start: 94 End: 124 Full_Region: AGAGTCATATAAAAA AAGAGACTGGGACA AAA TGTCTCAGTCTCGC TTTATCGTATTCACA .............................................................................................AAGAGACTGGGACAAAATGTCTCAGTCTCGC.................................................................... TransTerm Strand: + Conf: 87 HP_score: -12.5 Tail_Score: -3.03348 Start: 95 End: 123 Full_Region: GAGTCATATAAAAAA AGAGACTGGGACA AAA TGTCTCAGTCTCG CTTTATCGTATTCAC ..............................................................................................AGAGACTGGGACAAAATGTCTCAGTCTCG..................................................................... TransTerm Strand: - Conf: 100 HP_score: -13.8 Tail_Score: -5.72616 Start: 96 End: 122 Full_Region: tgaatacgataaagc gagactgagaca ttt tgtcccagtctc tttttttatatgact ...............................................................................................gagactgagacattttgtcccagtctc...................................................................... TransTerm Strand: + Conf: 86 HP_score: -12.8 Tail_Score: -2.73268 Start: 98 End: 120 Full_Region: TCATATAAAAAAAGA GACTGGGACA AAA TGTCTCAGTC TCGCTTTATCGTATT .................................................................................................GACTGGGACAAAATGTCTCAGTC........................................................................ Find igs database================================================ Query_seq: SSA_1949:SSA_1950|SSA_1949:SSA_1950:AliA protein, putative:ABC-type oligopeptide transport system, periplasmic component, putative:<-<-:1944464..1944655 192 aaacttcctccagttttcattaagattactttcattatagcacttctgtgacaggatgtaaacgcttcaatgcaatagagagtcatataaaaaaagagactgggacaaaatgtctcagtctcgctttatcgtattcacaaacttttgattccaaactgtttataaagaatcaaaaattcgcggttcagaacc Intra-Species Hit: Count: 1 Min: 1 Max: 192 Len: 192 Subject: NC_009009_SSA_1949_SSA_1950|AliA protein, putative:ABC-type oligopeptide transport system, periplasmic component, putative|NEGATIVE:NEGATIVE|[1944464,1944655]|192 HSP 1 e-value: 2.0E-92 bit: 339.0 Len: 192 Query Start:1 Query End:192 Subject Strand: POSITIVE Subject Start: 1 Subject End: 192 aaacttcctccagttttcattaagattactttcattatagcacttctgtgacaggatgtaaacgcttcaatgcaatagagagtcatatnnnnnnngagactgggacaaaatgtctcagtctcgctttatcgtattcacaaacttttgattccaaactgtttataaagaatcaaaaattcgcggttcagaacc aaacttcctccagttttcattaagattactttcattatagcacttctgtgacaggatgtaaacgcttcaatgcaatagagagtcatataaaaaaagagactgggacaaaatgtctcagtctcgctttatcgtattcacaaacttttgattccaaactgtttataaagaatcaaaaattcgcggttcagaacc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAACUUCCUCCAGUUUUCAUUAAGAUUACUUUCAUUAUAGCACUUCUGUGACAGGAUGUAAACGCUUCAAUGCAAUAGAGAGUCAUAUAAAAAAAGAGACUGGGACAAAAUGUCUCAGUCUCGCUUUAUCGUAUUCACAAACUUUUGAUUCCAAACUGUUUAUAAAGAAUCAAAAAUUCGCGGUUCAGAACC ..((.((((..(((..((.....))..)))..........(((....)))..)))).))...(((...(((((.((((((...............(((((((((((.....))))))))))).)))))).))))).......(((((((((...............)))))))))....))).......... (-43.55) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GGUUCUGAACCGCGAAUUUUUGAUUCUUUAUAAACAGUUUGGAAUCAAAAGUUUGUGAAUACGAUAAAGCGAGACUGAGACAUUUUGUCCCAGUCUCUUUUUUUAUAUGACUCUCUAUUGCAUUGAAGCGUUUACAUCCUGUCACAGAAGUGCUAUAAUGAAAGUAAUCUUAAUGAAAACUGGAGGAAGUUU ..........(((((((((((((((((..((.....))..)))))))))))))))))......((((((.(((((((.(((.....))).)))))))...))))))..((((..((....(((((.(((((((.....(((...)))))))))).)))))..(((..((.....))..)))..))..)))). (-46.80) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 860 80 31 171 122 NC_009009:SSA_1949|5end_AliA_protein,_putative_1944373..1944603_NEGATIVE 402 126 96 141 110 NC_009009:SSA_0680|5end_Serine/threonine_protein_phosphatase,_putative_662425..662655_POSITIVE 356 129 92 63 27 NC_009009:SSA_1575|5end_Glycosyl_transferase,_putative_1579110..1579340_NEGATIVE 337 158 111 135 72 NC_009009:SSA_0218|5end_Sugar-binding_periplasmic_protein,_putative_213863..214093_POSITIVE 319 122 92 207 178 NC_009009:SSA_0780|5end_Acid_phosphatase_(PAP2_family),_putative_764748..764978_POSITIVE 315 120 71 209 161 NC_009009:SSA_2393|5end_Transcriptional_regulator,_XRE_family,_putative_204056..204286_POSITIVE 313 137 92 197 156 NC_009009:SSA_0790|5end_hypothetical_protein_773047..773277_POSITIVE 305 130 95 150 112 NC_009009:SSA_1173|5end_Lipoate_protein_ligase_A,_putative_1201081..1201311_NEGATIVE 304 138 100 79 38 NC_009009:SSA_2334|5end_D-alanine--D-alanyl_carrier_protein_ligase,_putative_2338007..2338237_NEGATIVE 276 129 95 214 184 NC_009009:SSA_0854|5end_hypothetical_protein_841335..841565_POSITIVE 266 129 88 167 124 NC_009009:SSA_1796|5end_Transcription_elongation_factor_GreA,_putative_1778307..1778537_NEGATIVE 260 108 71 115 76 NC_009009:SSA_1191|5end_hypothetical_protein_1218323..1218553_NEGATIVE 260 150 101 76 8 NC_009009:SSA_0749|5end_Competence_protein,_putative_730668..730898_POSITIVE 257 105 63 212 152 NC_009009:SSA_1102|5end_hypothetical_protein_1123386..1123616_POSITIVE 256 67 28 214 176 NC_009009:SSA_0264|5end_PEP_phosphonomutase-like_protein,_putative_258400..258630_POSITIVE 254 46 5 99 64 NC_009009:SSA_1261|5end_Ribose-5-phosphate_isomerase_A,_putative_1287654..1287884_NEGATIVE 254 140 93 63 14 NC_009009:SSA_0810|5end_P-loop_ATPase,_putative_791582..791812_POSITIVE 252 138 95 88 48 NC_009009:SSA_2141|5end_Argininosuccinate_lyase,_putative_2142201..2142431_NEGATIVE 252 47 1 96 51 NC_009009:SSA_1010|5end_UDP-glucose_4-epimerase,_putative_1012739..1012969_POSITIVE 252 43 7 131 99 NC_009009:SSA_0321|5end_Methylase,_putative_313867..314097_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 497 137 92 59 13 NC_009009:SSA_0956|3end_surface_protein_D_965418..965568_POSITIVE 402 126 96 88 57 NC_009009:SSA_0679|3end_DNA_repair_and_genetic_recombination,_putative_662452..662602_POSITIVE 367 129 82 79 33 NC_009009:SSA_1909|3end_Transcriptional_attenuator_LytR,_putative_1900904..1901054_NEGATIVE 337 158 111 138 75 NC_009009:SSA_0217|3end_Two-component_system_transcriptional_regulator_(CheY_domain_and_HTH-like_DNA-binding_domain),_putative_213946..214096_POSITIVE 319 122 92 64 35 NC_009009:SSA_0779|3end_Glycogen_phosphorylase,_putative_764685..764835_POSITIVE 312 120 72 85 34 NC_009009:SSA_0876|3end_4-methyl-5(B-hydroxyethyl)-thiazole_monophosphate_biosynthesis_protein,_putative_870861..871011_POSITIVE 310 131 95 98 60 NC_009009:SSA_1729|3end_ABC_transporter_substrate-binding_protein-branched_chain_amino_acid_transport,_putative_1714539..1714689_NEGATIVE 305 130 95 83 45 NC_009009:SSA_1174|3end_Dihydrolipoamide_dehydrogenase,_putative_1201148..1201298_NEGATIVE 304 138 100 59 18 NC_009009:SSA_2335|3end_D-Ala-teichoic_acid_biosynthesis_protein,_putative_2338027..2338177_NEGATIVE 297 190 155 107 73 NC_009009:SSA_1857|3end_Conserved_DivIVA-like_protein,_putative_1852725..1852875_NEGATIVE 297 139 93 100 56 NC_009009:SSA_0395|3end_6-phospho-beta-glucosidase,_putative_392580..392730_POSITIVE 291 137 93 104 58 NC_009009:SSA_2301|3end_S-layer_protein/_peptidoglycan_endo-beta-N-acetylglucosaminidase,_putative_2302669..2302819_NEGATIVE 285 50 4 144 96 NC_009009:SSA_0994|3end_Peptidase_E,_putative_995390..995540_POSITIVE 283 134 94 51 13 NC_009009:SSA_1409|3end_DTDP-glucose-4,6-dehydratase,_putative_1421209..1421359_NEGATIVE 278 130 91 81 39 NC_009009:SSA_1808|3end_hypothetical_protein_1791394..1791544_NEGATIVE 275 127 81 87 29 NC_009009:SSA_0349|3end_Transcriptional_regulator,_TetR/AcrR_family,_putative_341828..341978_POSITIVE 267 127 86 84 45 NC_009009:SSA_1630|3end_hypothetical_protein_1631508..1631658_POSITIVE 262 133 92 97 59 NC_009009:SSA_0599|3end_hypothetical_protein_589007..589157_POSITIVE 257 150 101 127 83 NC_009009:SSA_0413|3end_Anthranilate/para-aminobenzoate_synthases_component_I/_Chorismate_binding_enzyme,_putative_408315..408465_NEGATIVE 257 129 92 44 7 NC_009009:SSA_0182|3end_Endoglucanase,_putative_187407..187557_POSITIVE