Origin IGS: gtactgctaattttagcggtgcttttacaattattcgcatcttattttattgcttggttccaacgatccagagtgaaagtagttgcgaaaggtcacagaaaaatagtaaaactttttacgataaacagaaaaacgcttactcctgagctataataggaatagcaaataattgaaaggacattctgtt .........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 aacagaatgtcctttcaattatttgctattcctattatagctcaggagtaagcgtttttctgtttatcgtaaaaagttttactatttttctgtgacctttcgcaactactttcactctggatcgttggaaccaagcaataaaataagatgcgaataattgtaaaagcaccgctaaaattagcagtac Mask Tandem Repeat Region ================================================ gtactgctaattttagcggtgcttttacaattattcgcatcttattttattgcttggttccaacgatccagagtgaaagtagttgcgaaaggtcacagaaaaatagtaaaactttttacgataaacagaaaaacgcttactcctgagctataataggaatagcaaataattgaaaggacattctgtt Find is-nt database================================================ Query_seq: SSA_0166:SSA_0167|SSA_0166:SSA_0167:hypothetical protein:Hypothetical protein (Asparagine/proline-rich):->->:165207..165393 187 gtactgctaattttagcggtgcttttacaattattcgcatcttattttattgcttggttccaacgatccagagtgaaagtagttgcgaaaggtcacagaaaaatagtaaaactttttacgataaacagaaaaacgcttactcctgagctataataggaatagcaaataattgaaaggacattctgtt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0166:SSA_0167|SSA_0166:SSA_0167:hypothetical protein:Hypothetical protein (Asparagine/proline-rich):->->:165207..165393 187 gtactgctaattttagcggtgcttttacaattattcgcatcttattttattgcttggttccaacgatccagagtgaaagtagttgcgaaaggtcacagaaaaatagtaaaactttttacgataaacagaaaaacgcttactcctgagctataataggaatagcaaataattgaaaggacattctgtt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0166:SSA_0167|SSA_0166:SSA_0167:hypothetical protein:Hypothetical protein (Asparagine/proline-rich):->->:165207..165393 187 gtactgctaattttagcggtgcttttacaattattcgcatcttattttattgcttggttccaacgatccagagtgaaagtagttgcgaaaggtcacagaaaaatagtaaaactttttacgataaacagaaaaacgcttactcctgagctataataggaatagcaaataattgaaaggacattctgtt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gtactgctaattttagcggtgcttttacaattattcgcatcttattttattgcttggttccaacgatccagagtgaaagtagttgcgaaaggtcacagaaaaatagtaaaactttttacgataaacagaaaaacgcttactcctgagctataataggaatagcaaataattgaaaggacattctgtt Predict ORF larger than 30AA ================================================ Protein_Len: 38 Strand: + Start: 30 End: 143 ............................. M I R I L F Y C L V P T I Q S E S S C E R S Q K N S K T F Y D K Q K N A Y S ............................................ Protein_Len: 49 Strand: + Start: 4 End: 150 ... M L I L A V L L Q L F A S Y F I A W F Q R S R V K V V A K G H R K I V K L F T I N R K T L T P E L ..................................... gtactgctaattttagcggtgcttttacaattattcgcatcttattttattgcttggttccaacgatccagagtgaaagtagttgcgaaaggtcacagaaaaatagtaaaactttttacgataaacagaaaaacgcttactcctgagctataataggaatagcaaataattgaaaggacattctgtt 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================================================ gtactgctaattttagcggtgcttttacaattattcgcatcttattttattgcttggttccaacgatccagagtgaaagtagttgcgaaaggtcacagaaaaatagtaaaactttttacgataaacagaaaaacgcttactcctgagctataataggaatagcaaataattgaaaggacattctgtt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_0166:SSA_0167|SSA_0166:SSA_0167:hypothetical protein:Hypothetical protein (Asparagine/proline-rich):->->:165207..165393 187 gtactgctaattttagcggtgcttttacaattattcgcatcttattttattgcttggttccaacgatccagagtgaaagtagttgcgaaaggtcacagaaaaatagtaaaactttttacgataaacagaaaaacgcttactcctgagctataataggaatagcaaataattgaaaggacattctgtt Intra-Species Hit: Count: 1 Min: 1 Max: 187 Len: 187 Subject: NC_009009_SSA_0166_SSA_0167|hypothetical protein:Hypothetical protein (Asparagine/proline-rich)|POSITIVE:POSITIVE|[165207, 165393]|187 HSP 1 e-value: 1.0E-102 bit: 371.0 Len: 187 Query Start:1 Query End:187 Subject Strand: POSITIVE Subject Start: 1 Subject End: 187 gtactgctaattttagcggtgcttttacaattattcgcatcttattttattgcttggttccaacgatccagagtgaaagtagttgcgaaaggtcacagaaaaatagtaaaactttttacgataaacagaaaaacgcttactcctgagctataataggaatagcaaataattgaaaggacattctgtt gtactgctaattttagcggtgcttttacaattattcgcatcttattttattgcttggttccaacgatccagagtgaaagtagttgcgaaaggtcacagaaaaatagtaaaactttttacgataaacagaaaaacgcttactcctgagctataataggaatagcaaataattgaaaggacattctgtt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUACUGCUAAUUUUAGCGGUGCUUUUACAAUUAUUCGCAUCUUAUUUUAUUGCUUGGUUCCAACGAUCCAGAGUGAAAGUAGUUGCGAAAGGUCACAGAAAAAUAGUAAAACUUUUUACGAUAAACAGAAAAACGCUUACUCCUGAGCUAUAAUAGGAAUAGCAAAUAAUUGAAAGGACAUUCUGUU (((((((((....)))))))))...........((((((.((..(((((((.((.((.((....)).)))))))))))..)).)))))).....((((((.....(((((....)))))...............(((...(((((........)))))..))).................)))))). (-42.40) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AACAGAAUGUCCUUUCAAUUAUUUGCUAUUCCUAUUAUAGCUCAGGAGUAAGCGUUUUUCUGUUUAUCGUAAAAAGUUUUACUAUUUUUCUGUGACCUUUCGCAACUACUUUCACUCUGGAUCGUUGGAACCAAGCAAUAAAAUAAGAUGCGAAUAAUUGUAAAAGCACCGCUAAAAUUAGCAGUAC .......(((..((.(((((((((((...((.((((((.(((..(((((...................(((((....)))))........(((((....))))).........)))))((.((....)).)).))).)))..))).)).))))))))))).))..)))..((((....))))..... (-31.80) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 311 99 52 231 178 NC_009009:SSA_0834|5end_Accessory_secretory_protein_Asp2,_putative_819510..819740_POSITIVE 299 117 73 87 34 NC_009009:SSA_0021|5end_hypothetical_protein_26842..27072_POSITIVE 298 95 52 47 9 NC_009009:SSA_0813|5end_Thioredoxin_reductase,_putative_795406..795636_NEGATIVE 295 98 53 222 180 NC_009009:SSA_2329|5end_hypothetical_protein_2332262..2332492_POSITIVE 278 99 56 57 10 NC_009009:SSA_1120|5end_Two-component_sensor_kinase_(with_C-terminal_ATPase_domain),_putative_1145222..1145452_POSITIVE 278 85 46 179 142 NC_009009:SSA_0109|5end_50S_ribosomal_protein_L23,_putative_109439..109669_POSITIVE 273 150 112 66 29 NC_009009:SSA_1784|5end_Glutamate_racemase,_putative_1769897..1770127_NEGATIVE 267 94 51 67 19 NC_009009:SSA_2285|5end_hypothetical_protein_2287404..2287634_POSITIVE 264 87 41 57 2 NC_009009:SSA_1933|5end_(3R)-hydroxymyristoyl-[acyl_carrier_protein]_dehydratase,_putative_1921315..1921545_NEGATIVE 260 99 51 158 113 NC_009009:SSA_1137|5end_Dihydrolipoamide_dehydrogenase,_putative_1164375..1164605_POSITIVE 259 100 56 142 96 NC_009009:SSA_1773|5end_hypothetical_protein_1760092..1760322_NEGATIVE 254 94 52 61 26 NC_009009:SSA_1772|5end_hypothetical_protein_1759545..1759775_NEGATIVE 253 99 58 145 102 NC_009009:SSA_1793|5end_Histidine_kinase_(sensor_protein),_putative_1776361..1776591_NEGATIVE 253 88 49 63 29 NC_009009:SSA_1581|5end_Metal-binding_ABC_transporter_(probably_hemin),_putative_1583662..1583892_POSITIVE 251 97 51 59 18 NC_009009:SSA_2197|5end_hypothetical_protein_2197784..2198014_NEGATIVE 250 98 51 223 170 NC_009009:SSA_1085|5end_Dihydrodipicolinate_reductase,_putative_1102564..1102794_POSITIVE 249 74 47 67 42 NC_009009:SSA_1563|5end_Metal-dependent_hydrolase,_beta-lactamase_superfamily_I,_putative_1567256..1567486_NEGATIVE 249 50 3 102 58 NC_009009:SSA_1561|5end_Ribonuclease_III,_putative_1565883..1566113_NEGATIVE 248 95 51 71 20 NC_009009:SSA_0855|5end_O-acetylhomoserine_sulfhydrylase,_putative_841832..842062_POSITIVE 240 92 56 64 23 NC_009009:SSA_2338|5end_Conserved_uncharacterized_protein_2339272..2339502_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 278 99 56 60 13 NC_009009:SSA_1119|3end_Two-component_response_transcriptional_regulator_(CheY-like_receiver_and_AraC-type_DNA-binding_domains),_putative_1145305..1145455_POSITIVE 275 101 63 135 101 NC_009009:SSA_1680|3end_ABC-type_bacitracin_resistance_protein_A,_permease_component,_putative_1673200..1673350_NEGATIVE 264 87 41 60 5 NC_009009:SSA_1934|3end_Biotin_carboxyl_carrier_protein_of_acetyl-CoA_carboxylase,_putative_1921312..1921462_NEGATIVE 257 87 47 60 20 NC_009009:SSA_1212|3end_Ribose-phosphate_pyrophosphokinase_2,_putative_1236437..1236587_POSITIVE 254 94 52 71 36 NC_009009:SSA_1773|3end_hypothetical_protein_1759535..1759685_NEGATIVE 252 87 41 126 76 NC_009009:SSA_0613|3end_Glucosyltransferase,_putative_606633..606783_POSITIVE 251 56 16 114 76 NC_009009:SSA_1459|3end_RNA_methyltransferase,_putative_1466111..1466261_NEGATIVE 249 74 47 57 32 NC_009009:SSA_1564|3end_Histidine_kinase,_putative_1567266..1567416_NEGATIVE 246 24 1 92 69 NC_009009:SSA_0166|3end_hypothetical_protein_165146..165296_POSITIVE 240 92 56 71 30 NC_009009:SSA_2337|3end_hypothetical_protein_2339359..2339509_POSITIVE 236 93 53 150 113 NC_009009:SSA_0500|3end_Peptide_ABC_transporter,_permease_protein,_putative_501524..501674_POSITIVE 235 58 16 58 13 NC_009009:SSA_0660|3end_Cell_division_protein_DivIVA,_putative_644672..644822_POSITIVE 233 107 63 57 26 NC_009009:SSA_2124|3end_Dehydrogenase,_eukaryotic-like,_putative_2128557..2128707_NEGATIVE 232 99 52 46 2 NC_009009:SSA_1467|3end_Chorismate_synthase,_putative_1473127..1473277_NEGATIVE 232 58 15 104 65 NC_009009:SSA_0087|3end_V-type_sodium_ATPase,_subunit_E,_putative_88999..89149_POSITIVE 231 86 58 146 118 NC_009009:SSA_1794|3end_Two-component_response_transcriptional_regulator_(CheY-like_receiver_and_winged-helix_DNA-binding_domains),_putative_1776345..1776495_NEGATIVE 231 69 29 115 73 NC_009009:SSA_1698|3end_Galactose-6-phosphate_isomerase,_LacB_subunit,_putative_1690133..1690283_NEGATIVE 231 43 1 129 78 NC_009009:SSA_1324|3end_Ceramide_glucosyltransferase,_putative_1340428..1340578_NEGATIVE 230 86 41 80 32 NC_009009:SSA_2210|3end_Ribosomal_large_subunit_pseudouridine_synthase_D,_putative_2211454..2211604_POSITIVE 228 79 36 84 40 NC_009009:SSA_1938|3end_Enoyl-acyl_carrier_protein(ACP)_reductase,_putative_1924764..1924914_NEGATIVE