Origin IGS: tttagatcttcaatttttttagattatagaaagggtgtgacatgcgaggacaatttttgtctttacaggatcactctttttttctttgttttataatcaaataagtcctctctttaaaactgtggtataataagtact .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 agtacttattataccacagttttaaagagaggacttatttgattataaaacaaagaaaaaaagagtgatcctgtaaagacaaaaattgtcctcgcatgtcacaccctttctataatctaaaaaaattgaagatctaaa Mask Tandem Repeat Region ================================================ tttagatcttcaatttttttagattatagaaagggtgtgacatgcgaggacaatttttgtctttacaggatcactctttttttctttgttttataatcaaataagtcctctctttaaaactgtggtataataagtact Find is-nt database================================================ Query_seq: SSA_1074:SSA_1075|SSA_1074:SSA_1075:Pyrroline-5-carboxylate reductase, putative:Coproporphyrinogen III oxidase, putative:->->:1093095..1093232 138 tttagatcttcaatttttttagattatagaaagggtgtgacatgcgaggacaatttttgtctttacaggatcactctttttttctttgttttataatcaaataagtcctctctttaaaactgtggtataataagtact Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1074:SSA_1075|SSA_1074:SSA_1075:Pyrroline-5-carboxylate reductase, putative:Coproporphyrinogen III oxidase, putative:->->:1093095..1093232 138 tttagatcttcaatttttttagattatagaaagggtgtgacatgcgaggacaatttttgtctttacaggatcactctttttttctttgttttataatcaaataagtcctctctttaaaactgtggtataataagtact Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1074:SSA_1075|SSA_1074:SSA_1075:Pyrroline-5-carboxylate reductase, putative:Coproporphyrinogen III oxidase, putative:->->:1093095..1093232 138 tttagatcttcaatttttttagattatagaaagggtgtgacatgcgaggacaatttttgtctttacaggatcactctttttttctttgttttataatcaaataagtcctctctttaaaactgtggtataataagtact Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tttagatcttcaatttttttagattatagaaagggtgtgacatgcgaggacaatttttgtctttacaggatcactctttttttctttgttttataatcaaataagtcctctctttaaaactgtggtataataagtact Predict ORF larger than 30AA ================================================ tttagatcttcaatttttttagattatagaaagggtgtgacatgcgaggacaatttttgtctttacaggatcactctttttttctttgttttataatcaaataagtcctctctttaaaactgtggtataataagtact 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================================================ tttagatcttcaatttttttagattatagaaagggtgtgacatgcgaggacaatttttgtctttacaggatcactctttttttctttgttttataatcaaataagtcctctctttaaaactgtggtataataagtact Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 85 HP_score: -2.3 Tail_Score: -6.11392 Start: 35 End: 76 Full_Region: TAGATTATAGAAAGG GTGTGACATGCGAGGACAA TTT TTGTCTTTACAGGATCACTC TTTTTTTCTTTGTTT ..................................GTGTGACATGCGAGGACAATTTTTGTCTTTACAGGATCACTC.............................................................. Find igs database================================================ Query_seq: SSA_1074:SSA_1075|SSA_1074:SSA_1075:Pyrroline-5-carboxylate reductase, putative:Coproporphyrinogen III oxidase, putative:->->:1093095..1093232 138 tttagatcttcaatttttttagattatagaaagggtgtgacatgcgaggacaatttttgtctttacaggatcactctttttttctttgttttataatcaaataagtcctctctttaaaactgtggtataataagtact Intra-Species Hit: Count: 1 Min: 21 Max: 138 Len: 118 Subject: NC_009009_SSA_1074_SSA_1075|Pyrroline-5-carboxylate reductase, putative:Coproporphyrinogen III oxidase, putative|POSITIVE:POSITIVE|[1093095,1093232]|138 HSP 1 e-value: 2.0E-48 bit: 192.0 Len: 118 Query Start:21 Query End:138 Subject Strand: POSITIVE Subject Start: 21 Subject End: 138 ....................agattatagaaagggtgtgacatgcgaggacaatttttgtctttacaggatcactcnnnnnnnctttgttttataatcaaataagtcctctctttaaaactgtggtataataagtact ....................agattatagaaagggtgtgacatgcgaggacaatttttgtctttacaggatcactctttttttctttgttttataatcaaataagtcctctctttaaaactgtggtataataagtact Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGAUUAUAGAAAGGGUGUGACAUGCGAGGACAAUUUUUGUCUUUACAGGAUCACUCUUUUUUUCUUUGUUUUAUAAUCAAAUAAGUCCUCUCUUUAAAACUGUGGUAUAAUAAGUACU .((((((((((((((((.....((..((((((.....))))))..))....)))))))))...........))))))).........................(((((.....))))) (-24.00) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGUACUUAUUAUACCACAGUUUUAAAGAGAGGACUUAUUUGAUUAUAAAACAAAGAAAAAAAGAGUGAUCCUGUAAAGACAAAAAUUGUCCUCGCAUGUCACACCCUUUCUAUAAUCU .....................(((.(((((((.(((.(((..((........))..))).))).(((((..((..(.((((.....)))).)..)).)))))..))))))).)))... (-18.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 291 65 21 108 66 NC_009009:SSA_0928|5end_ABC-type_multidrug_transporter,_ATPase_and_permease_components,_putative_936679..936909_POSITIVE 263 69 23 118 71 NC_009009:SSA_1897|5end_Ribosomal_protein_HS6-type_(S12/L30/L7a),_putative_1894450..1894680_NEGATIVE 250 59 12 73 26 NC_009009:SSA_0302|5end_Phosphoglycerate_kinase,_putative_294890..295120_POSITIVE 249 88 42 131 81 NC_009009:SSA_0874|5end_hypothetical_protein_867935..868165_POSITIVE 249 107 61 117 61 NC_009009:SSA_0561|5end_RNA:NAD_2'-phosphotransferase,_putative_553630..553860_POSITIVE 247 57 13 173 130 NC_009009:SSA_0417|5end_5,10-methylenetetrahydrofolate_reductase,_putative_414280..414510_POSITIVE 242 47 4 152 108 NC_009009:SSA_0272|5end_Oxidoreductase,_aldo/keto_reductase_family,_putative_266023..266253_POSITIVE 240 70 23 223 164 NC_009009:SSA_2226|5end_Organic_radical_activating_chaperone,_putative_2227756..2227986_NEGATIVE 238 48 6 189 143 NC_009009:SSA_1114|5end_Histidine_kinase,_putative_1140437..1140667_POSITIVE 231 67 27 96 53 NC_009009:SSA_2085|5end_Glyoxylate_reductase,_NADH-dependent,_putative_2090404..2090634_NEGATIVE 230 48 11 118 78 NC_009009:SSA_1769|5end_hypothetical_protein_1757490..1757720_NEGATIVE 228 80 31 130 61 NC_009009:SSA_1322|5end_Glycosyl_transferase,_putative_1339819..1340049_NEGATIVE 224 64 21 161 111 NC_009009:SSA_1650|5end_3-Ketoacyl-ACP_reductase,_putative_1649594..1649824_NEGATIVE 223 48 11 54 11 NC_009009:SSA_0118|5end_50S_ribosomal_protein_L24,_putative_113363..113593_POSITIVE 221 98 52 141 98 NC_009009:SSA_2230|5end_Ribonucleotide_reductase,_class_III,_anaerobic,_putative_2231158..2231388_NEGATIVE 221 44 12 62 24 NC_009009:SSA_1841|5end_Cof_family_protein/peptidyl-prolyl_cis-trans_isomerase,_cyclophilin_type,_putative_1835822..1836052_NEGATIVE 219 46 6 214 163 NC_009009:SSA_1624|5end_hypothetical_protein_1626070..1626300_POSITIVE 219 69 24 70 25 NC_009009:SSA_0936|5end_FAD_synthase,_putative_945139..945369_POSITIVE 218 69 24 107 66 NC_009009:SSA_1845|5end_Serine/threonine_protein_kinase,_putative_1840181..1840411_NEGATIVE 217 110 61 123 79 NC_009009:SSA_1064|5end_hypothetical_protein_1081065..1081295_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 291 65 21 89 47 NC_009009:SSA_0927|3end_Transcriptional_regulator,_TetR/AcrR_family,_putative_936740..936890_POSITIVE 263 69 23 125 78 NC_009009:SSA_1899|3end_hypothetical_protein_1894443..1894593_NEGATIVE 262 68 22 123 65 NC_009009:SSA_0263|3end_Zinc_metalloproteinase_in_scaA_5'region,_putative_258246..258396_POSITIVE 249 107 61 124 68 NC_009009:SSA_0560|3end_hypothetical_protein_553717..553867_POSITIVE 247 58 12 76 21 NC_009009:SSA_0686|3end_Fe2+/Zn2+_uptake_regulation_protein,_putative_670079..670229_POSITIVE 242 47 4 142 98 NC_009009:SSA_0271|3end_Glycosylhydrolase,_family_35,_putative_266093..266243_POSITIVE 231 67 27 103 60 NC_009009:SSA_2086|3end_hypothetical_protein_2090397..2090547_NEGATIVE 230 48 11 124 84 NC_009009:SSA_1770|3end_hypothetical_protein_1757484..1757634_NEGATIVE 224 68 24 88 50 NC_009009:SSA_1008|3end_Galactokinase,_putative_1011114..1011264_POSITIVE 224 57 26 35 6 NC_009009:SSA_0416|3end_5-methyltetrahydropteroyltriglutamate--_homocysteine_methyltransferase,_putative_414222..414372_POSITIVE 219 47 2 45 9 NC_009009:SSA_2227|3end_Acetyl_transferase,_putative_2227716..2227866_NEGATIVE 218 69 24 110 69 NC_009009:SSA_1846|3end_Phosphoprotein_phosphatase,_putative_1840178..1840328_NEGATIVE 213 65 23 92 49 NC_009009:SSA_1467|3end_Chorismate_synthase,_putative_1473127..1473277_NEGATIVE 212 107 76 142 107 NC_009009:SSA_1438|3end_Acetyltransferase,_putative_1443142..1443292_NEGATIVE 211 60 11 105 41 NC_009009:SSA_0445|3end_hypothetical_protein_444776..444926_POSITIVE 209 66 21 74 31 NC_009009:SSA_2261|3end_Transcriptional_repressor_(arginine_synthesis),_putative_2258229..2258379_NEGATIVE 208 59 11 61 13 NC_009009:SSA_1074|3end_Pyrroline-5-carboxylate_reductase,_putative_1093034..1093184_POSITIVE 206 60 12 118 58 NC_009009:SSA_1026|3end_ABC-type_multidrug_transporter,_ATPase_component,_putative_1043617..1043767_POSITIVE 205 93 51 146 105 NC_009009:SSA_0636|3end_N-(5'-phosphoribosyl)anthranilate_isomerase,_putative_625809..625959_POSITIVE 203 68 21 148 99 NC_009009:SSA_0533|3end_Glycerol_dehydratase_large_subunit_pduC,_putative_530711..530861_POSITIVE