Origin IGS: gcaaacctcctttgatagaatcttaaaaatttagaaaattctcatgaaaagtataccatattttcaactgtgtaacaagctatggaaaaaatacaattaaaatcagaaaaattatggttggtttttccatacagttctaggaaccgtaaccaaagataatacttgagcataccaaggtaaggtgacaatgtaaaaagccctctgaaaatcagagagctgatttgagctcgggctaaaatcctagtgaaacaaaaaaat .........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 atttttttgtttcactaggattttagcccgagctcaaatcagctctctgattttcagagggctttttacattgtcaccttaccttggtatgctcaagtattatctttggttacggttcctagaactgtatggaaaaaccaaccataatttttctgattttaattgtattttttccatagcttgttacacagttgaaaatatggtatacttttcatgagaattttctaaatttttaagattctatcaaaggaggtttgc Mask Tandem Repeat Region ================================================ gcaaacctcctttgatagaatcttaaaaatttagaaaattctcatgaaaagtataccatattttcaactgtgtaacaagctatggaaaaaatacaattaaaatcagaaaaattatggttggtttttccatacagttctaggaaccgtaaccaaagataatacttgagcataccaaggtaaggtgacaatgtaaaaagccctctgaaaatcagagagctgatttgagctcgggctaaaatcctagtgaaacaaaaaaat Find is-nt database================================================ Query_seq: SMT_963:SMT_964|SMT_963:SMT_964:K02015 iron complex transport system permease protein:cadmium resistance transporter, putative:<-<-:909723..909980 258 gcaaacctcctttgatagaatcttaaaaatttagaaaattctcatgaaaagtataccatattttcaactgtgtaacaagctatggaaaaaatacaattaaaatcagaaaaattatggttggtttttccatacagttctaggaaccgtaaccaaagataatacttgagcataccaaggtaaggtgacaatgtaaaaagccctctgaaaatcagagagctgatttgagctcgggctaaaatcctagtgaaacaaaaaaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_963:SMT_964|SMT_963:SMT_964:K02015 iron complex transport system permease protein:cadmium resistance transporter, putative:<-<-:909723..909980 258 gcaaacctcctttgatagaatcttaaaaatttagaaaattctcatgaaaagtataccatattttcaactgtgtaacaagctatggaaaaaatacaattaaaatcagaaaaattatggttggtttttccatacagttctaggaaccgtaaccaaagataatacttgagcataccaaggtaaggtgacaatgtaaaaagccctctgaaaatcagagagctgatttgagctcgggctaaaatcctagtgaaacaaaaaaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_963:SMT_964|SMT_963:SMT_964:K02015 iron complex transport system permease protein:cadmium resistance transporter, putative:<-<-:909723..909980 258 gcaaacctcctttgatagaatcttaaaaatttagaaaattctcatgaaaagtataccatattttcaactgtgtaacaagctatggaaaaaatacaattaaaatcagaaaaattatggttggtttttccatacagttctaggaaccgtaaccaaagataatacttgagcataccaaggtaaggtgacaatgtaaaaagccctctgaaaatcagagagctgatttgagctcgggctaaaatcctagtgaaacaaaaaaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gcaaacctcctttgatagaatcttaaaaatttagaaaattctcatgaaaagtataccatattttcaactgtgtaacaagctatggaaaaaatacaattaaaatcagaaaaattatggttggtttttccatacagttctaggaaccgtaaccaaagataatacttgagcataccaaggtaaggtgacaatgtaaaaagccctctgaaaatcagagagctgatttgagctcgggctaaaatcctagtgaaacaaaaaaat Predict ORF larger than 30AA ================================================ Protein_Len: 60 Strand: - Start: 45 End: 239 ............................................ N E V T Y C A I S F I C N F D S F N H N T K G Y L E L F R L W L Y Y K L M G L Y P S L T F L G R F I L S S I Q A R A L M ................... gcaaacctcctttgatagaatcttaaaaatttagaaaattctcatgaaaagtataccatattttcaactgtgtaacaagctatggaaaaaatacaattaaaatcagaaaaattatggttggtttttccatacagttctaggaaccgtaaccaaagataatacttgagcataccaaggtaaggtgacaatgtaaaaagccctctgaaaatcagagagctgatttgagctcgggctaaaatcctagtgaaacaaaaaaat 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: 83 Start: 50 End: 79 .................................................CTTGTTACACAGTTGAAAATATGGTATACT................................................................................................................................................................................... PromScan Matrix: RpoD-17 Strand: - Score: 81 Start: 166 End: 195 .....................................................................................................................................................................TTTTACATTGTCACCTTACCTTGGTATGCT............................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ gcaaacctcctttgatagaatcttaaaaatttagaaaattctcatgaaaagtataccatattttcaactgtgtaacaagctatggaaaaaatacaattaaaatcagaaaaattatggttggtttttccatacagttctaggaaccgtaaccaaagataatacttgagcataccaaggtaaggtgacaatgtaaaaagccctctgaaaatcagagagctgatttgagctcgggctaaaatcctagtgaaacaaaaaaat Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 100 HP_score: -11.9 Tail_Score: -4.78149 Start: 197 End: 217 Full_Region: cccgagctcaaatca gctctctga ttt tcagagggc tttttacattgtcac ....................................................................................................................................................................................................gctctctgattttcagagggc......................................... Find igs database================================================ Query_seq: SMT_963:SMT_964|SMT_963:SMT_964:K02015 iron complex transport system permease protein:cadmium resistance transporter, putative:<-<-:909723..909980 258 gcaaacctcctttgatagaatcttaaaaatttagaaaattctcatgaaaagtataccatattttcaactgtgtaacaagctatggaaaaaatacaattaaaatcagaaaaattatggttggtttttccatacagttctaggaaccgtaaccaaagataatacttgagcataccaaggtaaggtgacaatgtaaaaagccctctgaaaatcagagagctgatttgagctcgggctaaaatcctagtgaaacaaaaaaat Intra-Species Hit: Count: 1 Min: 1 Max: 250 Len: 250 Subject: smit_SMT_963_SMT_964|K02015 iron complex transport system permease protein:cadmium resistance transporter, putative|NEGATIVE:NEGATIVE|[909723,909980]|258 HSP 1 e-value: 1.0E-139 bit: 496.0 Len: 250 Query Start:1 Query End:250 Subject Strand: POSITIVE Subject Start: 1 Subject End: 250 gcaaacctcctttgatagaatcttaaaaatttagaaaattctcatgaaaagtataccatattttcaactgtgtaacaagctatggaaaaaatacaattaaaatcagaaaaattatggttggtttttccatacagttctaggaaccgtaaccaaagataatacttgagcataccaaggtaaggtgacaatgtaaaaagccctctgaaaatcagagagctgatttgagctcgggctaaaatcctagtgaaac........ gcaaacctcctttgatagaatcttaaaaatttagaaaattctcatgaaaagtataccatattttcaactgtgtaacaagctatggaaaaaatacaattaaaatcagaaaaattatggttggtttttccatacagttctaggaaccgtaaccaaagataatacttgagcataccaaggtaaggtgacaatgtaaaaagccctctgaaaatcagagagctgatttgagctcgggctaaaatcctagtgaaac........ Inter-species Hit: Count: 4 Min: 130 Max: 249 Len: 120 Subject: NC_009009_SSA_2056_SSA_2058|Cinnamoyl ester hydrolase, putative:30S ribosomal protein S15, putative|POSITIVE:NEGATIVE|[2059654,2060147]|494 HSP 1 e-value: 1.0E-20 bit: 101.0 Len: 120 Query Start:130 Query End:249 Subject Strand: POSITIVE Subject Start: 293 Subject End: 413 .................................................................................................................................tacagttctaggaaccgtaaccaaagataatacttgagcataccaaggtaaggtgac--aatgtaaaaagccctctgaaaatcagagagctgatttgagctcgggctaaaatcctagtgaaa......... .................................................................................................................................tacagtgctaggaaccgtaaccgaagataatacttgagtatatcgaggtaaggtgacggaacagaaaaagctccctg-aagtcagagagccaatttgagctcgggctaaaatcctagtgaaa......... Subject: NC_008533_SPD_1438_SPD_1439|cadmium resistance transporter, putative:ribosomal protein S15|NEGATIVE:NEGATIVE|[1456387,1457119]|733 HSP 1 e-value: 3.0E-15 bit: 83.8 Len: 58 Query Start:192 Query End:249 Subject Strand: POSITIVE Subject Start: 343 Subject End: 399 ...............................................................................................................................................................................................aaaaagccctctgaaaatcagagagctgatttgagctcgggctaaaatcctagtgaaa......... ...............................................................................................................................................................................................aaaaagccctctgaag-tcagagagctgatttgagcccgggctaaaatcctagtgaaa......... HSP 2 e-value: 2.0E-13 bit: 77.8 Len: 59 Query Start:130 Query End:188 Subject Strand: POSITIVE Subject Start: 593 Subject End: 651 .................................................................................................................................tacagttctaggaaccgtaaccaaagataatacttgagcataccaaggtaaggtgacaa...................................................................... .................................................................................................................................tacagtgctaggaaccgtaaccaaagattatacttgagtatagcgaggtaaggtgacaa...................................................................... Subject: NC_003098_spr1466_spr1467|Confers low level cadmium resistance in Staphylococcus aureus:30S ribosomal protein S15|NEGATIVE:NEGATIVE|[1448856,1449588]|733 HSP 1 e-value: 3.0E-15 bit: 83.8 Len: 58 Query Start:192 Query End:249 Subject Strand: POSITIVE Subject Start: 343 Subject End: 399 ...............................................................................................................................................................................................aaaaagccctctgaaaatcagagagctgatttgagctcgggctaaaatcctagtgaaa......... ...............................................................................................................................................................................................aaaaagccctctgaag-tcagagagctgatttgagcccgggctaaaatcctagtgaaa......... HSP 2 e-value: 2.0E-13 bit: 77.8 Len: 59 Query Start:130 Query End:188 Subject Strand: POSITIVE Subject Start: 593 Subject End: 651 .................................................................................................................................tacagttctaggaaccgtaaccaaagataatacttgagcataccaaggtaaggtgacaa...................................................................... .................................................................................................................................tacagtgctaggaaccgtaaccaaagattatacttgagtatagcgaggtaaggtgacaa...................................................................... Subject: NC_003028_SP_1625_SP_1626|cadmium resistance transporter, putative:30S ribosomal protein S15|NEGATIVE:NEGATIVE|[1527453,1528267]|815 HSP 1 e-value: 3.0E-15 bit: 83.8 Len: 58 Query Start:192 Query End:249 Subject Strand: POSITIVE Subject Start: 344 Subject End: 400 ...............................................................................................................................................................................................aaaaagccctctgaaaatcagagagctgatttgagctcgggctaaaatcctagtgaaa......... ...............................................................................................................................................................................................aaaaagccctctgaag-tcagagagctgatttgagcccgggctaaaatcctagtgaaa......... HSP 2 e-value: 2.0E-13 bit: 77.8 Len: 59 Query Start:130 Query End:188 Subject Strand: POSITIVE Subject Start: 594 Subject End: 652 .................................................................................................................................tacagttctaggaaccgtaaccaaagataatacttgagcataccaaggtaaggtgacaa...................................................................... .................................................................................................................................tacagtgctaggaaccgtaaccaaagattatacttgagtatatcgaggtaaggtgacaa...................................................................... Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UACAGUUCUAGGAACCGUAACCAAAGAUAAUACUUGAGCAUACCAAGGUAAGGUGACAAUGUAAAAAGCCCUCUGAAAAUCAGAGAGCUGAUUUGAGCUCGGGCUAAAAUCCUAGUGAAA .......((((((...((.(((.(((......))).....(((....))).))).)).........(((((.(((.....))).(((((......))))))))))....))))))..... (-29.60) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUCACUAGGAUUUUAGCCCGAGCUCAAAUCAGCUCUCUGAUUUUCAGAGGGCUUUUUACAUUGUCACCUUACCUUGGUAUGCUCAAGUAUUAUCUUUGGUUACGGUUCCUAGAACUGUA .....(((((((..(((((.((((.......(((((((((.....)))))))))............(((.......)))..)))).((......))..)))))..).))))))....... (-33.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 330 120 71 72 13 smit:SMT_796|5end_K03734_thiamine_biosynthesis_lipoprotein_704211..704441_POSITIVE 315 105 68 176 126 smit:SMT_1488|5end_K06147_ATP-binding_cassette,_subfamily_B,_bacterial_1467157..1467387_POSITIVE 310 117 71 174 118 smit:SMT_366|5end_hypothetical_protein_302085..302315_POSITIVE 303 106 67 90 44 smit:SMT_926|5end_guanylate_kinase_880934..881164_NEGATIVE 302 105 71 163 120 smit:SMT_1963|5end_ribonuclease_BN,_putative_1896462..1896692_NEGATIVE 302 105 71 198 155 smit:SMT_1810|5end_hypothetical_protein_1785219..1785449_POSITIVE 302 105 71 215 172 smit:SMT_1179|5end_aldose_1-epimerase_1137854..1138084_NEGATIVE 302 105 71 150 107 smit:SMT_483|5end_transcriptional_activator_TipA,_putative_418827..419057_POSITIVE 288 105 71 161 118 smit:SMT_1782|5end_hypothetical_protein_1759520..1759750_POSITIVE 281 103 63 168 111 smit:SMT_1544|5end_mevalonate_kinase_1528884..1529114_NEGATIVE 279 99 54 167 115 smit:SMT_970|5end_threonyl-tRNA_synthetase_915772..916002_POSITIVE 279 116 72 62 10 smit:SMT_265|5end_DNA-binding_protein_204073..204303_NEGATIVE 276 57 11 187 147 smit:SMT_1602|5end_hypothetical_protein_1592385..1592615_POSITIVE 276 105 71 151 108 smit:SMT_1200|5end_K06148_ATP-binding_cassette,_subfamily_C,_bacterial_1163235..1163465_NEGATIVE 276 105 71 212 169 smit:SMT_1138|5end_hypothetical_protein_1079547..1079777_NEGATIVE 276 57 11 212 172 smit:SMT_833|5end_hypothetical_protein_predicted_by_Glimmer/Critica_775362..775592_NEGATIVE 276 57 11 196 156 smit:SMT_130|5end_capsular_polysaccharide_biosynthesis_protein_80995..81225_POSITIVE 273 72 35 117 82 smit:SMT_1095|5end_ribosomal_large_subunit_pseudouridine_synthase,_RluD_subfamily_1036373..1036603_POSITIVE 272 89 46 218 168 smit:SMT_1605|5end_hypothetical_protein_1595406..1595636_POSITIVE 269 104 71 231 189 smit:SMT_443|5end_hydroxyethylthiazole_kinase_382555..382785_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 605 59 11 63 15 smit:SMT_969|3end_30S_ribosomal_protein_S15_914653..914803_NEGATIVE 296 57 11 57 17 smit:SMT_915|3end_sucrose_operon_repressor_868619..868769_POSITIVE 283 116 72 66 17 smit:SMT_1075|3end_hypothetical_protein_1013870..1014020_POSITIVE 280 57 11 52 12 smit:SMT_1964|3end_sodium/hydrogen_exchanger_family_protein_1896596..1896746_NEGATIVE 276 57 11 57 17 smit:SMT_834|3end_hypothetical_protein_775517..775667_NEGATIVE 276 57 11 56 16 smit:SMT_698|3end_uracil_permease_609769..609919_POSITIVE 275 57 11 52 12 smit:SMT_1536|3end_trigger_factor_1520636..1520786_NEGATIVE 274 57 15 33 2 smit:SMT_1671|3end_hypothetical_protein_1659392..1659542_NEGATIVE 270 116 72 62 13 smit:SMT_451|3end_thiamine-phosphate_pyrophosphorylase_389647..389797_POSITIVE 265 113 82 39 11 smit:SMT_547|3end_branched-chain_amino_acid_aminotransferase_465049..465199_POSITIVE 262 102 68 69 35 smit:SMT_2006|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1926803..1926953_POSITIVE 262 115 74 70 33 smit:SMT_1278|3end_30S_ribosomal_protein_S2_1242332..1242482_POSITIVE 262 118 71 122 63 smit:SMT_260|3end_phage_transcriptional_repressor_200236..200386_POSITIVE 260 68 21 59 10 smit:SMT_1046|3end_chaperonin_GroEL_987638..987788_NEGATIVE 254 57 15 38 7 smit:SMT_1487|3end_hypothetical_protein_1467076..1467226_POSITIVE 254 56 11 53 14 smit:SMT_799|3end_hypothetical_protein_707296..707446_NEGATIVE 250 56 11 55 16 smit:SMT_1809|3end_MutT/NUDIX_family_protein_1785134..1785284_POSITIVE 247 45 2 55 13 smit:SMT_1606|3end_glutamate_racemase_1596731..1596881_POSITIVE 245 104 68 63 19 smit:SMT_468|3end_ABC-type_oligopeptide_transport_system,_periplasmic_component_404903..405053_POSITIVE 245 104 68 80 36 smit:SMT_461|3end_mannose-6-phosphate_isomerase_400403..400553_POSITIVE