Origin IGS: tttataaatcccctttttcctaaaatgtataaagctaatctcccattatctctctagccaactccccagcaggctaaaaagatgcgttttatacatatagtattatcatatatcttttaggaaatttttacaatagattttacttaaaaaaacaattaatttttataaaagtaaatagagaaaatctctttacactttttatagtgaatttcttttgattaaagggctgatcagagctgctctcttttttgactacatttgcccaatagccttctaggaaacataaaaaggacagcattaggctgttcctttttatatga .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9 tcatataaaaaggaacagcctaatgctgtcctttttatgtttcctagaaggctattgggcaaatgtagtcaaaaaagagagcagctctgatcagccctttaatcaaaagaaattcactataaaaagtgtaaagagattttctctatttacttttataaaaattaattgtttttttaagtaaaatctattgtaaaaatttcctaaaagatatatgataatactatatgtataaaacgcatctttttagcctgctggggagttggctagagagataatgggagattagctttatacattttaggaaaaaggggatttataaa Mask Tandem Repeat Region ================================================ tttataaatcccctttttcctaaaatgtataaagctaatctcccattatctctctagccaactccccagcaggctaaaaagatgcgttttatacatatagtattatcatatatcttttaggaaatttttacaatagattttacttaaaaaaacaattaatttttataaaagtaaatagagaaaatctctttacactttttatagtgaatttcttttgattaaagggctgatcagagctgctctcttttttgactacatttgcccaatagccttctaggaaacataaaaaggacagcattaggctgttcctttttatatga Find is-nt database================================================ Query_seq: SSA_2004:SSA_2005|SSA_2004:SSA_2005:Zinc metalloprotease zmpB precursor, putative:Chaperone protein dnaJ, putative:<-<-:2005021..2005340 320 tttataaatcccctttttcctaaaatgtataaagctaatctcccattatctctctagccaactccccagcaggctaaaaagatgcgttttatacatatagtattatcatatatcttttaggaaatttttacaatagattttacttaaaaaaacaattaatttttataaaagtaaatagagaaaatctctttacactttttatagtgaatttcttttgattaaagggctgatcagagctgctctcttttttgactacatttgcccaatagccttctaggaaacataaaaaggacagcattaggctgttcctttttatatga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_2004:SSA_2005|SSA_2004:SSA_2005:Zinc metalloprotease zmpB precursor, putative:Chaperone protein dnaJ, putative:<-<-:2005021..2005340 320 tttataaatcccctttttcctaaaatgtataaagctaatctcccattatctctctagccaactccccagcaggctaaaaagatgcgttttatacatatagtattatcatatatcttttaggaaatttttacaatagattttacttaaaaaaacaattaatttttataaaagtaaatagagaaaatctctttacactttttatagtgaatttcttttgattaaagggctgatcagagctgctctcttttttgactacatttgcccaatagccttctaggaaacataaaaaggacagcattaggctgttcctttttatatga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_2004:SSA_2005|SSA_2004:SSA_2005:Zinc metalloprotease zmpB precursor, putative:Chaperone protein dnaJ, putative:<-<-:2005021..2005340 320 tttataaatcccctttttcctaaaatgtataaagctaatctcccattatctctctagccaactccccagcaggctaaaaagatgcgttttatacatatagtattatcatatatcttttaggaaatttttacaatagattttacttaaaaaaacaattaatttttataaaagtaaatagagaaaatctctttacactttttatagtgaatttcttttgattaaagggctgatcagagctgctctcttttttgactacatttgcccaatagccttctaggaaacataaaaaggacagcattaggctgttcctttttatatga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tttataaatcccctttttcctaaaatgtataaagctaatctcccattatctctctagccaactccccagcaggctaaaaagatgcgttttatacatatagtattatcatatatcttttaggaaatttttacaatagattttacttaaaaaaacaattaatttttataaaagtaaatagagaaaatctctttacactttttatagtgaatttcttttgattaaagggctgatcagagctgctctcttttttgactacatttgcccaatagccttctaggaaacataaaaaggacagcattaggctgttcctttttatatga Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: + Start: 8 End: 97 ....... M P F F L K C I K L I S H Y L S S Q L P S R L K R C V L Y I ............................................................................................................................................................................................................................... Protein_Len: 38 Strand: + Start: 102 End: 215 ..................................................................................................... M I I Y L L G N F Y N R F Y L K K Q L I F I K V N R E N L F T L F I V N F F ......................................................................................................... Protein_Len: 58 Strand: - Start: 143 End: 316 .............................................................................................................................................. K F F C N I K I F T F L S F R K V S K I T F K K Q N F P Q D S S S E K K V V N A W Y G E L F C L F S L M L S N R K M .... tttataaatcccctttttcctaaaatgtataaagctaatctcccattatctctctagccaactccccagcaggctaaaaagatgcgttttatacatatagtattatcatatatcttttaggaaatttttacaatagattttacttaaaaaaacaattaatttttataaaagtaaatagagaaaatctctttacactttttatagtgaatttcttttgattaaagggctgatcagagctgctctcttttttgactacatttgcccaatagccttctaggaaacataaaaaggacagcattaggctgttcctttttatatga 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: 82 Start: 105 End: 134 ........................................................................................................ATTGTAAAAATTTCCTAAAAGATATATGAT.......................................................................................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tttataaatcccctttttcctaaaatgtataaagctaatctcccattatctctctagccaactccccagcaggctaaaaagatgcgttttatacatatagtattatcatatatcttttaggaaatttttacaatagattttacttaaaaaaacaattaatttttataaaagtaaatagagaaaatctctttacactttttatagtgaatttcttttgattaaagggctgatcagagctgctctcttttttgactacatttgcccaatagccttctaggaaacataaaaaggacagcattaggctgttcctttttatatga Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_2004:SSA_2005|SSA_2004:SSA_2005:Zinc metalloprotease zmpB precursor, putative:Chaperone protein dnaJ, putative:<-<-:2005021..2005340 320 tttataaatcccctttttcctaaaatgtataaagctaatctcccattatctctctagccaactccccagcaggctaaaaagatgcgttttatacatatagtattatcatatatcttttaggaaatttttacaatagattttacttaaaaaaacaattaatttttataaaagtaaatagagaaaatctctttacactttttatagtgaatttcttttgattaaagggctgatcagagctgctctcttttttgactacatttgcccaatagccttctaggaaacataaaaaggacagcattaggctgttcctttttatatga Intra-Species Hit: Count: 1 Min: 1 Max: 320 Len: 320 Subject: NC_009009_SSA_2004_SSA_2005|Zinc metalloprotease zmpB precursor, putative:Chaperone protein dnaJ, putative|NEGATIVE:NEGATIVE|[2005021,2005340]|320 HSP 1 e-value: 1.0E-168 bit: 593.0 Len: 320 Query Start:1 Query End:320 Subject Strand: POSITIVE Subject Start: 1 Subject End: 320 tttataaatcccctttttcctaaaatgtataaagctaatctcccattatctctctagccaactccccagcaggctaaaaagatgcgttttatacatatagtattatcatatatcttttaggaaatttttacaatagattttacttnnnnnnncaattaatttttataaaagtaaatagagaaaatctctttacactttttatagtgaatttcttttgattaaagggctgatcagagctgctctcttttttgactacatttgcccaatagccttctaggaaacataaaaaggacagcattaggctgttcctttttatatga tttataaatcccctttttcctaaaatgtataaagctaatctcccattatctctctagccaactccccagcaggctaaaaagatgcgttttatacatatagtattatcatatatcttttaggaaatttttacaatagattttacttaaaaaaacaattaatttttataaaagtaaatagagaaaatctctttacactttttatagtgaatttcttttgattaaagggctgatcagagctgctctcttttttgactacatttgcccaatagccttctaggaaacataaaaaggacagcattaggctgttcctttttatatga Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUAUAAAUCCCCUUUUUCCUAAAAUGUAUAAAGCUAAUCUCCCAUUAUCUCUCUAGCCAACUCCCCAGCAGGCUAAAAAGAUGCGUUUUAUACAUAUAGUAUUAUCAUAUAUCUUUUAGGAAAUUUUUACAAUAGAUUUUACUUAAAAAAACAAUUAAUUUUUAUAAAAGUAAAUAGAGAAAAUCUCUUUACACUUUUUAUAGUGAAUUUCUUUUGAUUAAAGGGCUGAUCAGAGCUGCUCUCUUUUUUGACUACAUUUGCCCAAUAGCCUUCUAGGAAACAUAAAAAGGACAGCAUUAGGCUGUUCCUUUUUAUAUGA ........(((....((((((((((((((((((((...........(((((.(.(((((..((....))..))))).).))))).)))))))))))...((((......))))..)))))))))......(((.(((.((((((..(((((........)))))..((((((....((((.....))))....))))))...))))))..))).)))......((((.((((((((..(....)..)))))).....)).))))............)))...((((((((((((((.....)))).)))))))))).... (-63.60) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCAUAUAAAAAGGAACAGCCUAAUGCUGUCCUUUUUAUGUUUCCUAGAAGGCUAUUGGGCAAAUGUAGUCAAAAAAGAGAGCAGCUCUGAUCAGCCCUUUAAUCAAAAGAAAUUCACUAUAAAAAGUGUAAAGAGAUUUUCUCUAUUUACUUUUAUAAAAAUUAAUUGUUUUUUUAAGUAAAAUCUAUUGUAAAAAUUUCCUAAAAGAUAUAUGAUAAUACUAUAUGUAUAAAACGCAUCUUUUUAGCCUGCUGGGGAGUUGGCUAGAGAGAUAAUGGGAGAUUAGCUUUAUACAUUUUAGGAAAAAGGGGAUUUAUAAA ..((((((((((((.((((.....))))))))))))))))((((((((.(..((..((((...((....))....((((.....)))).....))))..))..).....................((((((((............(((((((....((((((.....))))))..)))))))............(((((((((....(((((((.......))))))).........((((((((((((.(((....))).))))))))))))..)))))))))..))))))))..))))))))................ (-82.10) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 956 90 41 181 132 NC_009009:SSA_2004|5end_Zinc_metalloprotease_zmpB_precursor,_putative_2004930..2005160_NEGATIVE 372 89 51 41 7 NC_009009:SSA_1583|5end_6-O-methylguanine-DNA_methyltransferase,_putative_1586026..1586256_NEGATIVE 343 270 225 121 70 NC_009009:SSA_0495|5end_ABC-type_oligopeptide/nickel_transport_system,_ATPase_component,_putative_495186..495416_POSITIVE 319 249 203 104 51 NC_009009:SSA_1438|5end_Acetyltransferase,_putative_1443612..1443842_NEGATIVE 310 87 41 61 11 NC_009009:SSA_0720|5end_hypothetical_protein_705106..705336_POSITIVE 307 305 261 187 153 NC_009009:SSA_0672|5end_hypothetical_protein_655191..655421_POSITIVE 301 299 257 180 143 NC_009009:SSA_0760|5end_Acetylornithine_aminotransferase,_putative_742581..742811_POSITIVE 296 74 34 121 81 NC_009009:SSA_1564|5end_Histidine_kinase,_putative_1568615..1568845_NEGATIVE 296 256 211 188 149 NC_009009:SSA_1207|5end_Phosphate_acetyltransferase,_putative_1232274..1232504_NEGATIVE 296 88 52 185 136 NC_009009:SSA_0486|5end_Uroporphyrinogen-III_synthase,_putative_486637..486867_POSITIVE 295 275 233 103 61 NC_009009:SSA_0258|5end_hypothetical_protein_251845..252075_POSITIVE 294 57 11 147 96 NC_009009:SSA_2217|5end_Cps9H,_putative_2219045..2219275_NEGATIVE 293 270 225 212 162 NC_009009:SSA_0102|5end_Kinase,_putative_104035..104265_POSITIVE 288 263 222 64 6 NC_009009:SSA_1994|5end_CTP_synthase,_putative_1992474..1992704_NEGATIVE 286 279 232 51 13 NC_009009:SSA_0433|5end_Methenyl_tetrahydrofolate_cyclohydrolase,_putative_435654..435884_NEGATIVE 285 239 196 130 85 NC_009009:SSA_2001|5end_Hydroxymethylpyrimidine/phosphomethylpyrimidine_kinase,_putative_1998220..1998450_NEGATIVE 285 76 32 162 113 NC_009009:SSA_1483|5end_Sphingosine_kinase_(diacylglycerol_kinase),_putative_1490220..1490450_NEGATIVE 284 278 236 135 92 NC_009009:SSA_1601|5end_VacB-like_protein,_putative_1607059..1607289_NEGATIVE 283 277 231 206 149 NC_009009:SSA_0089|5end_V-type_sodium_ATPase,_subunit_F,_putative_89930..90160_POSITIVE 282 97 51 62 16 NC_009009:SSA_1122|5end_Thioredoxin_family_protein,_putative_1147871..1148101_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 343 270 225 124 73 NC_009009:SSA_0494|3end_ABC-type_dipeptide/oligopeptide/nickel_transport_system,_ATPase_component,_putative_495269..495419_POSITIVE 319 249 203 92 39 NC_009009:SSA_1439|3end_hypothetical_protein_1443624..1443774_NEGATIVE 307 89 47 89 40 NC_009009:SSA_1253|3end_hypothetical_protein_1280976..1281126_NEGATIVE 296 270 222 56 6 NC_009009:SSA_1676|3end_Transcriptional_regulator,_LytTr_family,_putative_1670858..1671008_NEGATIVE 296 74 34 128 88 NC_009009:SSA_1565|3end_Two-component_response_transcriptional_regulator_(CheY-like_receiver_and_winged-helix_DNA-binding_domains),_putative_1568608..1568758_NEGATIVE 294 57 11 69 18 NC_009009:SSA_2218|3end_Glycosyltransferase_(cell_wall_biogenesis)_Cps9G,_putative_2219123..2219273_NEGATIVE 294 307 261 151 101 NC_009009:SSA_0394|3end_hypothetical_protein_390931..391081_POSITIVE 290 313 272 67 20 NC_009009:SSA_0419|3end_Alpha-galactosidase,_putative_418530..418680_POSITIVE 285 239 196 140 95 NC_009009:SSA_2002|3end_tRNA_pseudouridine_synthase_A,_putative_1998210..1998360_NEGATIVE 282 97 51 47 1 NC_009009:SSA_1121|3end_Cytochrome_C-type_biogenesis_protein,_putative_1147936..1148086_POSITIVE 280 305 261 112 63 NC_009009:SSA_1915|3end_hypothetical_protein_1905276..1905426_NEGATIVE 280 270 221 75 32 NC_009009:SSA_1836|3end_Superfamily_II_ATP-dependent_DNA/RNA_helicase_required_for_DNA_uptake_(late_competence_protein),_putative_1830938..1831088_NEGATIVE 279 309 268 135 94 NC_009009:SSA_1935|3end_Beta-ketoacyl-ACP_synthase_II_(3-oxoacyl-(Acyl-carrier-protein)_synthase_II),_putative_1921807..1921957_NEGATIVE 277 260 211 148 90 NC_009009:SSA_1476|3end_Phosphoglycerol_transferase,_alkaline_phosphatase_superfamily,_putative_1482448..1482598_POSITIVE 275 86 59 63 27 NC_009009:SSA_2337|3end_hypothetical_protein_2339359..2339509_POSITIVE 274 75 32 151 103 NC_009009:SSA_1484|3end_DNA_ligase,_putative_1490230..1490380_NEGATIVE 273 280 231 67 18 NC_009009:SSA_1085|3end_Dihydrodipicolinate_reductase,_putative_1103411..1103561_POSITIVE 273 279 232 122 67 NC_009009:SSA_0390|3end_hypothetical_protein_385714..385864_POSITIVE 268 270 225 55 8 NC_009009:SSA_0101|3end_Conserved_uncharacterized_protein_104113..104263_POSITIVE 267 309 261 151 96 NC_009009:SSA_1608|3end_hypothetical_protein_1613283..1613433_NEGATIVE