Origin IGS: taaaatatctgagaatggggttaaattatgaaaagaattgttaggaaaacaatgggctatacattgattctagctattgttgtgttctcttttagattatatatgatttccagtaaagaagtgtttgataatgcattatttactgattatttccaagtagatgaagctgaaaatggggga .........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 tcccccattttcagcttcatctacttggaaataatcagtaaataatgcattatcaaacacttctttactggaaatcatatataatctaaaagagaacacaacaatagctagaatcaatgtatagcccattgttttcctaacaattcttttcataatttaaccccattctcagatatttta Mask Tandem Repeat Region ================================================ taaaatatctgagaatggggttaaattatgaaaagaattgttaggaaaacaatgggctatacattgattctagctattgttgtgttctcttttagattatatatgatttccagtaaagaagtgtttgataatgcattatttactgattatttccaagtagatgaagctgaaaatggggga Find is-nt database================================================ Query_seq: FN0476:FN0477|FN0476:FN0477:transcription termination factor Rho:Cell wall endopeptidase family M23/M37:->->:1124832..1125011 180 taaaatatctgagaatggggttaaattatgaaaagaattgttaggaaaacaatgggctatacattgattctagctattgttgtgttctcttttagattatatatgatttccagtaaagaagtgtttgataatgcattatttactgattatttccaagtagatgaagctgaaaatggggga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN0476:FN0477|FN0476:FN0477:transcription termination factor Rho:Cell wall endopeptidase family M23/M37:->->:1124832..1125011 180 taaaatatctgagaatggggttaaattatgaaaagaattgttaggaaaacaatgggctatacattgattctagctattgttgtgttctcttttagattatatatgatttccagtaaagaagtgtttgataatgcattatttactgattatttccaagtagatgaagctgaaaatggggga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN0476:FN0477|FN0476:FN0477:transcription termination factor Rho:Cell wall endopeptidase family M23/M37:->->:1124832..1125011 180 taaaatatctgagaatggggttaaattatgaaaagaattgttaggaaaacaatgggctatacattgattctagctattgttgtgttctcttttagattatatatgatttccagtaaagaagtgtttgataatgcattatttactgattatttccaagtagatgaagctgaaaatggggga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taaaatatctgagaatggggttaaattatgaaaagaattgttaggaaaacaatgggctatacattgattctagctattgttgtgttctcttttagattatatatgatttccagtaaagaagtgtttgataatgcattatttactgattatttccaagtagatgaagctgaaaatggggga Predict ORF larger than 30AA ================================================ Protein_Len: 52 Strand: + Start: 25 End: 180 ........................ M M K R I V R K T M G Y T L I L A I V V F S F R L Y M I S S K E V F D N A L F T D Y F Q V D E A E N G G taaaatatctgagaatggggttaaattatgaaaagaattgttaggaaaacaatgggctatacattgattctagctattgttgtgttctcttttagattatatatgatttccagtaaagaagtgtttgataatgcattatttactgattatttccaagtagatgaagctgaaaatggggga 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================================================ taaaatatctgagaatggggttaaattatgaaaagaattgttaggaaaacaatgggctatacattgattctagctattgttgtgttctcttttagattatatatgatttccagtaaagaagtgtttgataatgcattatttactgattatttccaagtagatgaagctgaaaatggggga Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 55 HP_score: -2.3 Tail_Score: -4.2679 Start: 50 End: 66 Full_Region: aacaatagctagaat caatg tatagcc cattg ttttcctaacaattc .................................................caatgtatagcccattg.................................................................................................................. Find igs database================================================ Query_seq: FN0476:FN0477|FN0476:FN0477:transcription termination factor Rho:Cell wall endopeptidase family M23/M37:->->:1124832..1125011 180 taaaatatctgagaatggggttaaattatgaaaagaattgttaggaaaacaatgggctatacattgattctagctattgttgtgttctcttttagattatatatgatttccagtaaagaagtgtttgataatgcattatttactgattatttccaagtagatgaagctgaaaatggggga Intra-Species Hit: Count: 1 Min: 1 Max: 180 Len: 180 Subject: NC_003454_FN0476_FN0477|transcription termination factor Rho:Cell wall endopeptidase family M23/M37|POSITIVE:POSITIVE|[1124832,1125011]|180 HSP 1 e-value: 8.0E-98 bit: 357.0 Len: 180 Query Start:1 Query End:180 Subject Strand: POSITIVE Subject Start: 1 Subject End: 180 taaaatatctgagaatggggttaaattatgaaaagaattgttaggaaaacaatgggctatacattgattctagctattgttgtgttctcttttagattatatatgatttccagtaaagaagtgtttgataatgcattatttactgattatttccaagtagatgaagctgaaaatggggga taaaatatctgagaatggggttaaattatgaaaagaattgttaggaaaacaatgggctatacattgattctagctattgttgtgttctcttttagattatatatgatttccagtaaagaagtgtttgataatgcattatttactgattatttccaagtagatgaagctgaaaatggggga Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAAAUAUCUGAGAAUGGGGUUAAAUUAUGAAAAGAAUUGUUAGGAAAACAAUGGGCUAUACAUUGAUUCUAGCUAUUGUUGUGUUCUCUUUUAGAUUAUAUAUGAUUUCCAGUAAAGAAGUGUUUGAUAAUGCAUUAUUUACUGAUUAUUUCCAAGUAGAUGAAGCUGAAAAUGGGGGA ......((((((((..(((..((.........((.(((.(((((((...(((((.......))))).))))))).))).)).))..))))))))))).............(((((((..(((((........))))).)))))))....(..(((..(((......)))....)))..). (-32.30) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCCCCCAUUUUCAGCUUCAUCUACUUGGAAAUAAUCAGUAAAUAAUGCAUUAUCAAACACUUCUUUACUGGAAAUCAUAUAUAAUCUAAAAGAGAACACAACAAUAGCUAGAAUCAAUGUAUAGCCCAUUGUUUUCCUAACAAUUCUUUUCAUAAUUUAACCCCAUUCUCAGAUAUUUUA ......((((((((..........))))))))..((((((((.((((..........)).)).))))))))............((((....(((((..........((((...........))))..((((((.....)))))).....................)))))))))...... (-17.50) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 250 180 131 125 76 NC_003454:FN1780|5end_hypothetical_protein_261664..261894_NEGATIVE 237 180 132 70 26 NC_003454:FN1334|5end_N-acetylmuramoyl-L-alanine_amidase_1988619..1988849_NEGATIVE 237 97 52 186 138 NC_003454:FN1011|5end_MGPA_protein_1665660..1665890_NEGATIVE 222 101 68 111 83 NC_003454:FN0330|5end_SSU_ribosomal_protein_S9P_964583..964813_POSITIVE 221 179 132 174 127 NC_003454:FN1089|5end_hypothetical_protein_1733042..1733272_POSITIVE 220 80 34 220 172 NC_003454:FN1765|5end_pyruvate_kinase_259450..259680_NEGATIVE 218 89 45 152 106 NC_003454:FN1473|5end_N-acetylneuraminate_transporter_large_subunit_2155032..2155262_POSITIVE 216 97 53 205 163 NC_003454:FN0328|5end_Na(+)-linked_D-alanine_glycine_permease_963771..964001_NEGATIVE 214 107 62 124 73 NC_003454:FN0574|5end_Hypothetical_cytosolic_protein_1223521..1223751_POSITIVE 213 178 133 150 88 NC_003454:FN1146|5end_Hypothetical_exported_24-amino_acid_repeat_protein_1796466..1796696_NEGATIVE 213 106 68 118 82 NC_003454:FN1556|5end_Protein_Translation_Elongation_Factor_G_(EF-G)_79606..79836_NEGATIVE 209 93 52 112 67 NC_003454:FN2115|5end_hypothetical_protein_624843..625073_NEGATIVE 207 88 52 227 185 NC_003454:FN1126|5end_Acetyltransferase_1770287..1770517_NEGATIVE 202 96 53 108 72 NC_003454:FN1823|5end_Transcriptional_regulator,_TetR_family_311720..311950_POSITIVE 200 116 74 177 136 NC_003454:FN1004|5end_Transcriptional_regulator,_TetR_family_1659662..1659892_POSITIVE 197 90 49 65 30 NC_003454:FN0720|5end_elongation_factor_P_1376976..1377206_POSITIVE 197 110 70 116 84 NC_003454:FN1540|5end_Iron-sulfur_cluster-binding_protein_53055..53285_POSITIVE 196 59 15 155 105 NC_003454:FN1882|5end_hypothetical_protein_368560..368790_POSITIVE 195 180 131 77 25 NC_003454:FN0838|5end_hypothetical_protein_1500747..1500977_POSITIVE 194 39 2 208 170 NC_003454:FN0691|5end_hypothetical_protein_1346372..1346602_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 250 180 131 57 8 NC_003454:FN1781|3end_LytB_protein_261732..261882_NEGATIVE 222 101 68 95 67 NC_003454:FN0329|3end_50S_ribosomal_protein_L13_964647..964797_POSITIVE 221 179 132 147 100 NC_003454:FN1088|3end_NADH_oxidase_1733095..1733245_POSITIVE 218 89 45 128 82 NC_003454:FN1472|3end_N-acetylneuraminate-binding_protein_2155088..2155238_POSITIVE 217 100 51 94 41 NC_003454:FN1392|3end_SSU_ribosomal_protein_S16P_2049196..2049346_NEGATIVE 214 107 62 122 71 NC_003454:FN0573|3end_hypothetical_protein_1223599..1223749_POSITIVE 213 106 68 72 36 NC_003454:FN1557|3end_30S_ribosomal_protein_S7_79652..79802_NEGATIVE 202 96 53 45 9 NC_003454:FN1822|3end_Flavodoxin_311737..311887_POSITIVE 197 90 49 65 30 NC_003454:FN0719|3end_Hypothetical_cytosolic_protein_1377056..1377206_POSITIVE 197 110 70 73 41 NC_003454:FN1539|3end_Iron-sulfur_cluster-binding_protein_53092..53242_POSITIVE 192 94 68 48 22 NC_003454:FN0982|3end_bifunctional_phosphoribosylaminoimidazolecarboxamide_formyltransferase/IMP_cyclohydrolase_1634137..1634287_NEGATIVE 191 98 51 65 11 NC_003454:FN2038|3end_LSU_ribosomal_protein_L10P_547184..547334_NEGATIVE 189 159 113 53 7 NC_003454:FN0808|3end_Phosphoglycerate_mutase_1468655..1468805_POSITIVE 187 97 51 145 95 NC_003454:FN0446|3end_hypothetical_protein_1089404..1089554_POSITIVE 187 75 35 62 12 NC_003454:FN1538|3end_Arsenical_pump-driving_ATPase_51109..51259_NEGATIVE 184 89 41 64 14 NC_003454:FN0227|3end_hypothetical_protein_854114..854264_NEGATIVE 184 45 4 143 98 NC_003454:FN1674|3end_hypothetical_protein_172225..172375_POSITIVE 180 91 62 42 14 NC_003454:FN0206|3end_Activator_of_(R)-2-hydroxyglutaryl-CoA_dehydratase_833635..833785_POSITIVE 180 156 120 120 87 NC_003454:FN0152|3end_Ribonuclease_III_780812..780962_POSITIVE 180 43 6 55 12 NC_003454:FN0018|3end_hypothetical_protein_655978..656128_NEGATIVE