Origin IGS: gattaagcttcagtaaaaagctttgaaaatctagaatatatgaaaagtctgttatctcaacttttgttgggaataacaggctttttctttttcagagaaagctaagcattataagcagtcaaatgcttgaatttttcataaaattaaaaataagcttgtatttttctagcaaatatggtaaactattttagtaaaaaattatacaaaggagactgttg .........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 caacagtctcctttgtataattttttactaaaatagtttaccatatttgctagaaaaatacaagcttatttttaattttatgaaaaattcaagcatttgactgcttataatgcttagctttctctgaaaaagaaaaagcctgttattcccaacaaaagttgagataacagacttttcatatattctagattttcaaagctttttactgaagcttaatc Mask Tandem Repeat Region ================================================ gattaagcttcagtaaaaagctttgaaaatctagaatatatgaaaagtctgttatctcaacttttgttgggaataacaggctttttctttttcagagaaagctaagcattataagcagtcaaatgcttgaatttttcataaaattaaaaataagcttgtatttttctagcaaatatggtaaactattttagtaaaaaattatacaaaggagactgttg Find is-nt database================================================ Query_seq: SSA_0684:SSA_0685|SSA_0684:SSA_0685:Fibril-like structure subunit FibA, putative:hypothetical protein:->->:668954..669171 218 gattaagcttcagtaaaaagctttgaaaatctagaatatatgaaaagtctgttatctcaacttttgttgggaataacaggctttttctttttcagagaaagctaagcattataagcagtcaaatgcttgaatttttcataaaattaaaaataagcttgtatttttctagcaaatatggtaaactattttagtaaaaaattatacaaaggagactgttg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0684:SSA_0685|SSA_0684:SSA_0685:Fibril-like structure subunit FibA, putative:hypothetical protein:->->:668954..669171 218 gattaagcttcagtaaaaagctttgaaaatctagaatatatgaaaagtctgttatctcaacttttgttgggaataacaggctttttctttttcagagaaagctaagcattataagcagtcaaatgcttgaatttttcataaaattaaaaataagcttgtatttttctagcaaatatggtaaactattttagtaaaaaattatacaaaggagactgttg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0684:SSA_0685|SSA_0684:SSA_0685:Fibril-like structure subunit FibA, putative:hypothetical protein:->->:668954..669171 218 gattaagcttcagtaaaaagctttgaaaatctagaatatatgaaaagtctgttatctcaacttttgttgggaataacaggctttttctttttcagagaaagctaagcattataagcagtcaaatgcttgaatttttcataaaattaaaaataagcttgtatttttctagcaaatatggtaaactattttagtaaaaaattatacaaaggagactgttg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gattaagcttcagtaaaaagctttgaaaatctagaatatatgaaaagtctgttatctcaacttttgttgggaataacaggctttttctttttcagagaaagctaagcattataagcagtcaaatgcttgaatttttcataaaattaaaaataagcttgtatttttctagcaaatatggtaaactattttagtaaaaaattatacaaaggagactgttg Predict ORF larger than 30AA ================================================ Protein_Len: 51 Strand: + Start: 36 End: 188 ................................... M Y E K S V I S T F V G N N R L F L F Q R K L S I I S S Q M L E F F I K L K I S L Y F S S K Y G K L F .............................. gattaagcttcagtaaaaagctttgaaaatctagaatatatgaaaagtctgttatctcaacttttgttgggaataacaggctttttctttttcagagaaagctaagcattataagcagtcaaatgcttgaatttttcataaaattaaaaataagcttgtatttttctagcaaatatggtaaactattttagtaaaaaattatacaaaggagactgttg 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================================================ gattaagcttcagtaaaaagctttgaaaatctagaatatatgaaaagtctgttatctcaacttttgttgggaataacaggctttttctttttcagagaaagctaagcattataagcagtcaaatgcttgaatttttcataaaattaaaaataagcttgtatttttctagcaaatatggtaaactattttagtaaaaaattatacaaaggagactgttg Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 100 HP_score: -9.5 Tail_Score: -5.61881 Start: 47 End: 81 Full_Region: TAGAATATATGAAAA GTCTGTTATCTCAAC TTTT GTTGGGAATAACAGGC TTTTTCTTTTTCAGA ..............................................GTCTGTTATCTCAACTTTTGTTGGGAATAACAGGC......................................................................................................................................... TransTerm Strand: + Conf: 39 HP_score: -2.0 Tail_Score: -2.65772 Start: 112 End: 129 Full_Region: GAAAGCTAAGCATTA TAAGCA GTCAAA TGCTTG AATTTTTCATAAAAT ...............................................................................................................TAAGCAGTCAAATGCTTG......................................................................................... Find igs database================================================ Query_seq: SSA_0684:SSA_0685|SSA_0684:SSA_0685:Fibril-like structure subunit FibA, putative:hypothetical protein:->->:668954..669171 218 gattaagcttcagtaaaaagctttgaaaatctagaatatatgaaaagtctgttatctcaacttttgttgggaataacaggctttttctttttcagagaaagctaagcattataagcagtcaaatgcttgaatttttcataaaattaaaaataagcttgtatttttctagcaaatatggtaaactattttagtaaaaaattatacaaaggagactgttg Intra-Species Hit: Count: 1 Min: 1 Max: 218 Len: 218 Subject: NC_009009_SSA_0684_SSA_0685|Fibril-like structure subunit FibA, putative:hypothetical protein|POSITIVE:POSITIVE|[668954,669171]|218 HSP 1 e-value: 1.0E-120 bit: 432.0 Len: 218 Query Start:1 Query End:218 Subject Strand: POSITIVE Subject Start: 1 Subject End: 218 gattaagcttcagtaaaaagctttgaaaatctagaatatatgaaaagtctgttatctcaacttttgttgggaataacaggctttttctttttcagagaaagctaagcattataagcagtcaaatgcttgaatttttcataaaattaaaaataagcttgtatttttctagcaaatatggtaaactattttagtaaaaaattatacaaaggagactgttg gattaagcttcagtaaaaagctttgaaaatctagaatatatgaaaagtctgttatctcaacttttgttgggaataacaggctttttctttttcagagaaagctaagcattataagcagtcaaatgcttgaatttttcataaaattaaaaataagcttgtatttttctagcaaatatggtaaactattttagtaaaaaattatacaaaggagactgttg Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAUUAAGCUUCAGUAAAAAGCUUUGAAAAUCUAGAAUAUAUGAAAAGUCUGUUAUCUCAACUUUUGUUGGGAAUAACAGGCUUUUUCUUUUUCAGAGAAAGCUAAGCAUUAUAAGCAGUCAAAUGCUUGAAUUUUUCAUAAAAUUAAAAAUAAGCUUGUAUUUUUCUAGCAAAUAUGGUAAACUAUUUUAGUAAAAAAUUAUACAAAGGAGACUGUUG ......((((.(((......(((((((((............((((((((((((((((((((....)))))).))))))))))))))..)))))))))...)))))))......(((((((....(((((((((((....)))))).....))))).(((((..((...((.((.((((....)))).)).))....))..))))).....))))))). (-52.64) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CAACAGUCUCCUUUGUAUAAUUUUUUACUAAAAUAGUUUACCAUAUUUGCUAGAAAAAUACAAGCUUAUUUUUAAUUUUAUGAAAAAUUCAAGCAUUUGACUGCUUAUAAUGCUUAGCUUUCUCUGAAAAAGAAAAAGCCUGUUAUUCCCAACAAAAGUUGAGAUAACAGACUUUUCAUAUAUUCUAGAUUUUCAAAGCUUUUUACUGAAGCUUAAUC ....(((((..(((((((..(((((((...(((((........)))))..))))))))))))))..............((((((((....(((((((...........))))))).(((((.(((.....))).)))))((((((((..((((....)))).))))))))..))))))))......)))))....(((((((.....))))))).... (-42.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 316 87 48 228 189 NC_009009:SSA_2058|5end_30S_ribosomal_protein_S15,_putative_2060354..2060584_NEGATIVE 291 108 76 127 90 NC_009009:SSA_1450|5end_hypothetical_protein_1452710..1452940_NEGATIVE 288 107 61 154 97 NC_009009:SSA_0104|5end_Queuine_tRNA-ribosyltransferase,_putative_105593..105823_POSITIVE 273 126 86 142 94 NC_009009:SSA_0843|5end_hypothetical_protein_827682..827912_POSITIVE 269 90 41 73 27 NC_009009:SSA_0913|5end_Acetyltransferase,_putative_924195..924425_POSITIVE 258 93 57 231 200 NC_009009:SSA_2355|5end_Conserved_uncharacterized_protein_2356600..2356830_NEGATIVE 253 90 48 195 154 NC_009009:SSA_0998|5end_hypothetical_protein_998487..998717_POSITIVE 250 139 92 91 39 NC_009009:SSA_1561|5end_Ribonuclease_III,_putative_1565883..1566113_NEGATIVE 247 107 70 53 14 NC_009009:SSA_1153|5end_HemK_protein,_putative_1181838..1182068_POSITIVE 246 124 82 137 93 NC_009009:SSA_1085|5end_Dihydrodipicolinate_reductase,_putative_1102564..1102794_POSITIVE 242 108 63 188 142 NC_009009:SSA_2085|5end_Glyoxylate_reductase,_NADH-dependent,_putative_2090404..2090634_NEGATIVE 238 120 81 130 91 NC_009009:SSA_1490|5end_Ribonuclease_BN,_putative_1496732..1496962_NEGATIVE 238 102 62 210 163 NC_009009:SSA_0065|5end_Low_molecular_weight_phosphotyrosine_protein_phosphatase,_putative_67175..67405_POSITIVE 237 128 81 187 133 NC_009009:SSA_1975|5end_ABC-type_multidrug_transport_system,_ATPase_component,_putative_1971132..1971362_NEGATIVE 235 111 76 169 130 NC_009009:SSA_2184|5end_hypothetical_protein_2183754..2183984_NEGATIVE 235 119 79 176 128 NC_009009:SSA_0958|5end_hypothetical_protein_967273..967503_POSITIVE 234 118 76 70 35 NC_009009:SSA_0508|5end_Conserved_uncharacterized_protein,_possible_phosphoserine_phosphatase_506668..506898_POSITIVE 233 137 96 227 180 NC_009009:SSA_0915|5end_hypothetical_protein_927542..927772_POSITIVE 230 120 74 75 28 NC_009009:SSA_0995|5end_Antibiotic-resistance_protein,_alpha/beta_superfamily_hydrolase,_putative_995716..995946_POSITIVE 229 78 31 72 16 NC_009009:SSA_1824|5end_hypothetical_protein_1812746..1812976_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 374 85 42 48 4 NC_009009:SSA_0684|3end_Fibril-like_structure_subunit_FibA,_putative_668893..669043_POSITIVE 316 87 48 88 49 NC_009009:SSA_2059|3end_16S_rRNA_uridine-516_pseudouridylate_synthase,_putative_2060494..2060644_NEGATIVE 291 108 76 93 56 NC_009009:SSA_1451|3end_Exonuclease_RexA,_putative_1452744..1452894_NEGATIVE 283 110 62 134 75 NC_009009:SSA_1320|3end_hypothetical_protein_1336829..1336979_NEGATIVE 257 118 79 135 99 NC_009009:SSA_1750|3end_Extracellular_nuclease,_putative_1735673..1735823_NEGATIVE 253 88 43 89 28 NC_009009:SSA_1537|3end_Conserved_uncharacterized_protein_1544229..1544379_NEGATIVE 248 128 87 40 1 NC_009009:SSA_1051|3end_Spermidine/putrescine_ABC_transporter,_spermidine/putrescine-binding_protein,_putative_1066808..1066958_POSITIVE 247 107 70 53 14 NC_009009:SSA_1152|3end_Protein_chain_release_factor_A,_putative_1181918..1182068_POSITIVE 246 124 82 96 52 NC_009009:SSA_1084|3end_Conserved_uncharacterized_protein_1102603..1102753_POSITIVE 244 71 31 137 101 NC_009009:SSA_1206|3end_A/G-specific_adenine_glycosylase,_putative_1230071..1230221_NEGATIVE 238 120 81 82 43 NC_009009:SSA_1491|3end_Methionine_aminopeptidase_A,_putative_1496780..1496930_NEGATIVE 230 126 81 72 16 NC_009009:SSA_1562|3end_hypothetical_protein_1566005..1566155_NEGATIVE 226 108 62 127 76 NC_009009:SSA_1846|3end_Phosphoprotein_phosphatase,_putative_1840178..1840328_NEGATIVE 225 130 91 74 29 NC_009009:SSA_1788|3end_Integral_membrane_protein,_possible_receptor,_putative_1771656..1771806_NEGATIVE 225 131 91 64 29 NC_009009:SSA_0036|3end_Secreted_protein,_possible_function_in_cell-wall_metabolism_(amidase),_putative_42050..42200_NEGATIVE 224 130 83 140 98 NC_009009:SSA_1715|3end_Phosphoserine_aminotransferase,_putative_1701397..1701547_NEGATIVE 224 93 55 139 95 NC_009009:SSA_0910|3end_ABC-type_multidrug_transporter,_ATPase_component,_putative_922161..922311_POSITIVE 223 120 77 134 99 NC_009009:SSA_0906|3end_CshA-like_fibrillar_surface_protein_C_917411..917561_POSITIVE 223 130 92 146 110 NC_009009:SSA_0222|3end_PTS_system,_mannose-specific_IID_component,_putative_218133..218283_POSITIVE 222 137 93 80 33 NC_009009:SSA_2156|3end_Conserved_uncharacterized_protein_2156216..2156366_NEGATIVE