Origin IGS: aattttatcagcctatattatgtcttgaatgattattgggtttggcagacgacttctggttatttgagctatcattattggacatcgttatagctacctcagttcttacgcatttataatttcaaaaaaacgatagaaaactttctgtcgttttttcttgttttctagtaattatactaagtcatttagattcacctactttttctccaatgaagttgtctgtcagagactttccgaagaactcaattgatcttcactatccagttcttacaccagcaagatgatttcatcattgagaagagaaagcgttacaaatccttatcatatcagaggtttttatcccttcttgcccttctgatttaaaaatgttataattttttatgaaattgtctaaaaattctaatctttgctgttaaggaggtctgg .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9 ccagacctccttaacagcaaagattagaatttttagacaatttcataaaaaattataacatttttaaatcagaagggcaagaagggataaaaacctctgatatgataaggatttgtaacgctttctcttctcaatgatgaaatcatcttgctggtgtaagaactggatagtgaagatcaattgagttcttcggaaagtctctgacagacaacttcattggagaaaaagtaggtgaatctaaatgacttagtataattactagaaaacaagaaaaaacgacagaaagttttctatcgtttttttgaaattataaatgcgtaagaactgaggtagctataacgatgtccaataatgatagctcaaataaccagaagtcgtctgccaaacccaataatcattcaagacataatataggctgataaaatt Mask Tandem Repeat Region ================================================ aattttatcagcctatattatgtcttgaatgattattgggtttggcagacgacttctggttatttgagctatcattattggacatcgttatagctacctcagttcttacgcatttataatttcaaaaaaacgatagaaaactttctgtcgttttttcttgttttctagtaattatactaagtcatttagattcacctactttttctccaatgaagttgtctgtcagagactttccgaagaactcaattgatcttcactatccagttcttacaccagcaagatgatttcatcattgagaagagaaagcgttacaaatccttatcatatcagaggtttttatcccttcttgcccttctgatttaaaaatgttataattttttatgaaattgtctaaaaattctaatctttgctgttaaggaggtctgg Find is-nt database================================================ Query_seq: SSA_1577:SSA_1578|SSA_1577:SSA_1578:Proline dipeptidase, putative:ABC-type Fe3+-siderophore transport system, permease component, putative:->->:1581517..1581942 426 aattttatcagcctatattatgtcttgaatgattattgggtttggcagacgacttctggttatttgagctatcattattggacatcgttatagctacctcagttcttacgcatttataatttcaaaaaaacgatagaaaactttctgtcgttttttcttgttttctagtaattatactaagtcatttagattcacctactttttctccaatgaagttgtctgtcagagactttccgaagaactcaattgatcttcactatccagttcttacaccagcaagatgatttcatcattgagaagagaaagcgttacaaatccttatcatatcagaggtttttatcccttcttgcccttctgatttaaaaatgttataattttttatgaaattgtctaaaaattctaatctttgctgttaaggaggtctgg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1577:SSA_1578|SSA_1577:SSA_1578:Proline dipeptidase, putative:ABC-type Fe3+-siderophore transport system, permease component, putative:->->:1581517..1581942 426 aattttatcagcctatattatgtcttgaatgattattgggtttggcagacgacttctggttatttgagctatcattattggacatcgttatagctacctcagttcttacgcatttataatttcaaaaaaacgatagaaaactttctgtcgttttttcttgttttctagtaattatactaagtcatttagattcacctactttttctccaatgaagttgtctgtcagagactttccgaagaactcaattgatcttcactatccagttcttacaccagcaagatgatttcatcattgagaagagaaagcgttacaaatccttatcatatcagaggtttttatcccttcttgcccttctgatttaaaaatgttataattttttatgaaattgtctaaaaattctaatctttgctgttaaggaggtctgg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1577:SSA_1578|SSA_1577:SSA_1578:Proline dipeptidase, putative:ABC-type Fe3+-siderophore transport system, permease component, putative:->->:1581517..1581942 426 aattttatcagcctatattatgtcttgaatgattattgggtttggcagacgacttctggttatttgagctatcattattggacatcgttatagctacctcagttcttacgcatttataatttcaaaaaaacgatagaaaactttctgtcgttttttcttgttttctagtaattatactaagtcatttagattcacctactttttctccaatgaagttgtctgtcagagactttccgaagaactcaattgatcttcactatccagttcttacaccagcaagatgatttcatcattgagaagagaaagcgttacaaatccttatcatatcagaggtttttatcccttcttgcccttctgatttaaaaatgttataattttttatgaaattgtctaaaaattctaatctttgctgttaaggaggtctgg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aattttatcagcctatattatgtcttgaatgattattgggtttggcagacgacttctggttatttgagctatcattattggacatcgttatagctacctcagttcttacgcatttataatttcaaaaaaacgatagaaaactttctgtcgttttttcttgttttctagtaattatactaagtcatttagattcacctactttttctccaatgaagttgtctgtcagagactttccgaagaactcaattgatcttcactatccagttcttacaccagcaagatgatttcatcattgagaagagaaagcgttacaaatccttatcatatcagaggtttttatcccttcttgcccttctgatttaaaaatgttataattttttatgaaattgtctaaaaattctaatctttgctgttaaggaggtctgg Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: + Start: 158 End: 247 ............................................................................................................................................................. M F S S N Y T K S F R F T Y F F S N E V V C Q R L S E E L N ................................................................................................................................................................................... Protein_Len: 37 Strand: + Start: 171 End: 281 .......................................................................................................................................................................... M I L S H L D S P T F S P M K L S V R D F P K N S I D L H Y P V L T P A R ................................................................................................................................................. Protein_Len: 47 Strand: + Start: 220 End: 360 ........................................................................................................................................................................................................................... M S E T F R R T Q L I F T I Q F L H Q Q D D F I I E K R K R Y K S L S Y Q R F L S L L A L L I .................................................................. Protein_Len: 30 Strand: - Start: 293 End: 382 .................................................................................................................................................................................................................................................................................................... Q S S F A N C I R I M D S T K I G E Q G E S K F I N Y N K M ............................................ aattttatcagcctatattatgtcttgaatgattattgggtttggcagacgacttctggttatttgagctatcattattggacatcgttatagctacctcagttcttacgcatttataatttcaaaaaaacgatagaaaactttctgtcgttttttcttgttttctagtaattatactaagtcatttagattcacctactttttctccaatgaagttgtctgtcagagactttccgaagaactcaattgatcttcactatccagttcttacaccagcaagatgatttcatcattgagaagagaaagcgttacaaatccttatcatatcagaggtttttatcccttcttgcccttctgatttaaaaatgttataattttttatgaaattgtctaaaaattctaatctttgctgttaaggaggtctgg 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: 88 Start: 346 End: 375 .........................................................................................................................................................................................................................................................................................................................................................CTTGCCCTTCTGATTTAAAAATGTTATAAT................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aattttatcagcctatattatgtcttgaatgattattgggtttggcagacgacttctggttatttgagctatcattattggacatcgttatagctacctcagttcttacgcatttataatttcaaaaaaacgatagaaaactttctgtcgttttttcttgttttctagtaattatactaagtcatttagattcacctactttttctccaatgaagttgtctgtcagagactttccgaagaactcaattgatcttcactatccagttcttacaccagcaagatgatttcatcattgagaagagaaagcgttacaaatccttatcatatcagaggtttttatcccttcttgcccttctgatttaaaaatgttataattttttatgaaattgtctaaaaattctaatctttgctgttaaggaggtctgg Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 100 HP_score: -7.2 Tail_Score: -5.77677 Start: 131 End: 150 Full_Region: ATAATTTCAAAAAAA CGATAGAA AACT TTCTGTCG TTTTTTCTTGTTTTC ..................................................................................................................................CGATAGAAAACTTTCTGTCG.................................................................................................................................................................................................................................................................................... TransTerm Strand: - Conf: 82 HP_score: -5.0 Tail_Score: -5.48303 Start: 131 End: 150 Full_Region: gaaaacaagaaaaaa cgacagaa agtt ttctatcg tttttttgaaattat ..................................................................................................................................cgacagaaagttttctatcg.................................................................................................................................................................................................................................................................................... Find igs database================================================ Query_seq: SSA_1577:SSA_1578|SSA_1577:SSA_1578:Proline dipeptidase, putative:ABC-type Fe3+-siderophore transport system, permease component, putative:->->:1581517..1581942 426 aattttatcagcctatattatgtcttgaatgattattgggtttggcagacgacttctggttatttgagctatcattattggacatcgttatagctacctcagttcttacgcatttataatttcaaaaaaacgatagaaaactttctgtcgttttttcttgttttctagtaattatactaagtcatttagattcacctactttttctccaatgaagttgtctgtcagagactttccgaagaactcaattgatcttcactatccagttcttacaccagcaagatgatttcatcattgagaagagaaagcgttacaaatccttatcatatcagaggtttttatcccttcttgcccttctgatttaaaaatgttataattttttatgaaattgtctaaaaattctaatctttgctgttaaggaggtctgg Intra-Species Hit: Count: 1 Min: 1 Max: 426 Len: 426 Subject: NC_009009_SSA_1577_SSA_1578|Proline dipeptidase, putative:ABC-type Fe3+-siderophore transport system, permease component, putative|POSITIVE:POSITIVE|[1581517,1581942]|426 HSP 1 e-value: 0.0 bit: 803.0 Len: 426 Query Start:1 Query End:426 Subject Strand: POSITIVE Subject Start: 1 Subject End: 426 aattttatcagcctatattatgtcttgaatgattattgggtttggcagacgacttctggttatttgagctatcattattggacatcgttatagctacctcagttcttacgcatttataatttcnnnnnnncgatagaaaactttctgtcgttttttcttgttttctagtaattatactaagtcatttagattcacctactttttctccaatgaagttgtctgtcagagactttccgaagaactcaattgatcttcactatccagttcttacaccagcaagatgatttcatcattgagaagagaaagcgttacaaatccttatcatatcagaggtttttatcccttcttgcccttctgatttaaaaatgttataattttttatgaaattgtctaaaaattctaatctttgctgttaaggaggtctgg aattttatcagcctatattatgtcttgaatgattattgggtttggcagacgacttctggttatttgagctatcattattggacatcgttatagctacctcagttcttacgcatttataatttcaaaaaaacgatagaaaactttctgtcgttttttcttgttttctagtaattatactaagtcatttagattcacctactttttctccaatgaagttgtctgtcagagactttccgaagaactcaattgatcttcactatccagttcttacaccagcaagatgatttcatcattgagaagagaaagcgttacaaatccttatcatatcagaggtttttatcccttcttgcccttctgatttaaaaatgttataattttttatgaaattgtctaaaaattctaatctttgctgttaaggaggtctgg Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUUUUAUCAGCCUAUAUUAUGUCUUGAAUGAUUAUUGGGUUUGGCAGACGACUUCUGGUUAUUUGAGCUAUCAUUAUUGGACAUCGUUAUAGCUACCUCAGUUCUUACGCAUUUAUAAUUUCAAAAAAACGAUAGAAAACUUUCUGUCGUUUUUUCUUGUUUUCUAGUAAUUAUACUAAGUCAUUUAGAUUCACCUACUUUUUCUCCAAUGAAGUUGUCUGUCAGAGACUUUCCGAAGAACUCAAUUGAUCUUCACUAUCCAGUUCUUACACCAGCAAGAUGAUUUCAUCAUUGAGAAGAGAAAGCGUUACAAAUCCUUAUCAUAUCAGAGGUUUUUAUCCCUUCUUGCCCUUCUGAUUUAAAAAUGUUAUAAUUUUUUAUGAAAUUGUCUAAAAAUUCUAAUCUUUGCUGUUAAGGAGGUCUGG .........((((((.(((((.......)))))...))))))(((((((((((((((((......(((.(((.(((((((((...(((...((((.....))))...)))..............((((((((((((((....)))))))))))))).......))))))))).)))...((((.....))))......))).....)))..)))))))))))))).((((((((.(((((.(......).)))))..................(((((.((((....))))...((((..((((.....................((((((((..................))))))))...........((((((((....)))))))).......))))..)))))))))....)))))))).. (-93.07) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CCAGACCUCCUUAACAGCAAAGAUUAGAAUUUUUAGACAAUUUCAUAAAAAAUUAUAACAUUUUUAAAUCAGAAGGGCAAGAAGGGAUAAAAACCUCUGAUAUGAUAAGGAUUUGUAACGCUUUCUCUUCUCAAUGAUGAAAUCAUCUUGCUGGUGUAAGAACUGGAUAGUGAAGAUCAAUUGAGUUCUUCGGAAAGUCUCUGACAGACAACUUCAUUGGAGAAAAAGUAGGUGAAUCUAAAUGACUUAGUAUAAUUACUAGAAAACAAGAAAAAACGACAGAAAGUUUUCUAUCGUUUUUUUGAAAUUAUAAAUGCGUAAGAACUGAGGUAGCUAUAACGAUGUCCAAUAAUGAUAGCUCAAAUAACCAGAAGUCGUCUGCCAAACCCAAUAAUCAUUCAAGACAUAAUAUAGGCUGAUAAAAUU .((((((((((((...(((....(((((........((((.(((...((((((......))))))..((((((.((.................)))))))).......))).))))..(((((.((.(((((...((((....))))...(..((......))..).((((((((..........(((....))).((((.....))))..)))))))))))))..)).)))))..))))).....((((((....)))))).......((((((((((.((((....)))).))))))))))...........))).))))....)))))..(((((...(((((....((((((............((((.....))))............))))))...)))))..))))).)))........ (-85.98) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 295 70 21 74 25 NC_009009:SSA_0322|5end_Transcriptional_activator,_TipA_family,_putative_314717..314947_POSITIVE 294 119 76 127 75 NC_009009:SSA_0235|5end_Integrase/recombinase,_phage_associated,_putative_229561..229791_POSITIVE 293 184 141 194 142 NC_009009:SSA_2231|5end_Heme/copper-type_cytochrome/quinol_oxidases,_subunit_1,_putative_2232928..2233158_NEGATIVE 291 250 203 158 100 NC_009009:SSA_1736|5end_L-cysteine_desulfhydrase,_putative_1722619..1722849_NEGATIVE 291 89 46 180 133 NC_009009:SSA_0854|5end_hypothetical_protein_841335..841565_POSITIVE 286 70 23 156 107 NC_009009:SSA_0159|5end_hypothetical_protein_155000..155230_POSITIVE 276 354 316 64 27 NC_009009:SSA_1280|5end_hypothetical_protein_1301596..1301826_NEGATIVE 276 76 31 92 37 NC_009009:SSA_0789|5end_Proton-translocating_ATPase,_F1_sector,_epsilon_subunit,_putative_772451..772681_POSITIVE 275 120 79 72 22 NC_009009:SSA_0613|5end_Glucosyltransferase,_putative_601847..602077_POSITIVE 273 59 11 178 119 NC_009009:SSA_0895|5end_ATP-binding_cassette_transporter-like_protein,_putative_886466..886696_POSITIVE 270 290 244 69 25 NC_009009:SSA_1701|5end_Transcriptional_repressor_of_sugar_metabolism,_GlpR/DeoR_family,_putative_1692054..1692284_NEGATIVE 270 240 192 132 88 NC_009009:SSA_1222|5end_NTP_pyrophosphohydrolases_including_oxidative_damage_repair_enzymes,_putative_1245454..1245684_NEGATIVE 270 60 11 189 142 NC_009009:SSA_0546|5end_Phospho-2-dehydro-3-deoxyheptonate_aldolase_(DAHP_synthatase),_possibly_tyr-sensitive,_putative_540852..541082_POSITIVE 270 161 121 159 120 NC_009009:SSA_0067|5end_Acyltransferase_(yrhL-like_subfamily_of_SGNH-hydrolases),_putative_68005..68235_POSITIVE 269 339 291 167 129 NC_009009:SSA_2264|5end_hypothetical_protein_2261757..2261987_NEGATIVE 268 356 316 145 103 NC_009009:SSA_1307|5end_Trk_transporter_membrane-spanning_protein-K+_transport,_putative_1326270..1326500_NEGATIVE 268 310 262 155 109 NC_009009:SSA_0049|5end_Dihydroxyacetone_kinase_(Dak1),_putative_53612..53842_POSITIVE 267 234 195 213 170 NC_009009:SSA_0471|5end_CbiG_protein,_putative_473600..473830_POSITIVE 266 87 41 212 164 NC_009009:SSA_1583|5end_6-O-methylguanine-DNA_methyltransferase,_putative_1586026..1586256_NEGATIVE 264 296 251 187 136 NC_009009:SSA_0777|5end_Glycogen_biosynthesis_protein_GlgD,_putative_759430..759660_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 286 70 23 150 101 NC_009009:SSA_0158|3end_hypothetical_protein_155074..155224_POSITIVE 276 354 316 52 15 NC_009009:SSA_1281|3end_Uracil-DNA_glycosylase,_putative_1301608..1301758_NEGATIVE 276 76 31 84 29 NC_009009:SSA_0788|3end_Proton-translocating_ATPase,_F1_sector,_beta_subunit,_putative_772523..772673_POSITIVE 276 274 239 119 85 NC_009009:SSA_0413|3end_Anthranilate/para-aminobenzoate_synthases_component_I/_Chorismate_binding_enzyme,_putative_408315..408465_NEGATIVE 268 356 316 148 106 NC_009009:SSA_1308|3end_hypothetical_protein_1326267..1326417_NEGATIVE 267 299 251 143 88 NC_009009:SSA_0761|3end_Transcriptional_regulator,_XRE_family,_putative_744169..744319_POSITIVE 263 95 52 66 21 NC_009009:SSA_1393|3end_hypothetical_protein_1408414..1408564_NEGATIVE 260 298 260 72 36 NC_009009:SSA_1166|3end_hypothetical_protein_1192350..1192500_POSITIVE 259 70 22 140 82 NC_009009:SSA_0330|3end_hypothetical_protein_325162..325312_POSITIVE 257 248 203 148 98 NC_009009:SSA_1737|3end_Cystathionine_gamma-synthase,_putative_1722621..1722771_NEGATIVE 256 178 141 147 103 NC_009009:SSA_2233|3end_hypothetical_protein_2232967..2233117_NEGATIVE 256 253 221 97 65 NC_009009:SSA_0549|3end_ATP-dependent_DNA_helicase_recG,_transcription-repair_coupling_factor,_putative_545651..545801_POSITIVE 256 319 272 105 58 NC_009009:SSA_0500|3end_Peptide_ABC_transporter,_permease_protein,_putative_501524..501674_POSITIVE 252 71 39 48 11 NC_009009:SSA_2042|3end_hypothetical_protein_2046669..2046819_NEGATIVE 251 204 165 99 53 NC_009009:SSA_1669|3end_hypothetical_protein_1668095..1668245_NEGATIVE 251 109 67 82 33 NC_009009:SSA_1268|3end_Chorismate_mutase/prephenate_dehydratase,_putative_1291347..1291497_NEGATIVE 251 230 181 146 103 NC_009009:SSA_1029|3end_hypothetical_protein_1046167..1046317_NEGATIVE 250 230 181 120 71 NC_009009:SSA_1243|3end_Dihydroorotate_dehydrogenase_electron_transfer_subunit,_putative_1267398..1267548_NEGATIVE 250 59 12 144 85 NC_009009:SSA_1011|3end_hypothetical_protein_1014804..1014954_POSITIVE 249 90 43 148 79 NC_009009:SSA_1249|3end_hypothetical_protein_1273275..1273425_NEGATIVE