Origin IGS: acttcctccataaagatttactctcttgattataccatgaaaaggctacaaatcagcacagcaaactttataattgaaattcaattttttaacatattcactatgacatttttgttttttagtgctatactataggcaataatacatccgagcaaggaggatgttcacatggaagataaataactcattactaatgcaacccaactcttatccgagttaaataaaagtttccaaagctgcaaacagggtactgcagatgatactcgactacaagagctgctaaacactactataaaagagctcaaaaaagcggaaaag .........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 cttttccgcttttttgagctcttttatagtagtgtttagcagctcttgtagtcgagtatcatctgcagtaccctgtttgcagctttggaaacttttatttaactcggataagagttgggttgcattagtaatgagttatttatcttccatgtgaacatcctccttgctcggatgtattattgcctatagtatagcactaaaaaacaaaaatgtcatagtgaatatgttaaaaaattgaatttcaattataaagtttgctgtgctgatttgtagccttttcatggtataatcaagagagtaaatctttatggaggaagt Mask Tandem Repeat Region ================================================ acttcctccataaagatttactctcttgattataccatgaaaaggctacaaatcagcacagcaaactttataattgaaattcaattttttaacatattcactatgacatttttgttttttagtgctatactataggcaataatacatccgagcaaggaggatgttcacatggaagataaataactcattactaatgcaacccaactcttatccgagttaaataaaagtttccaaagctgcaaacagggtactgcagatgatactcgactacaagagctgctaaacactactataaaagagctcaaaaaagcggaaaag Find is-nt database================================================ Query_seq: SMT_692:SMT_693|SMT_692:SMT_693:hypothetical protein:hypothetical protein:<-->:603641..603958 318 acttcctccataaagatttactctcttgattataccatgaaaaggctacaaatcagcacagcaaactttataattgaaattcaattttttaacatattcactatgacatttttgttttttagtgctatactataggcaataatacatccgagcaaggaggatgttcacatggaagataaataactcattactaatgcaacccaactcttatccgagttaaataaaagtttccaaagctgcaaacagggtactgcagatgatactcgactacaagagctgctaaacactactataaaagagctcaaaaaagcggaaaag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_692:SMT_693|SMT_692:SMT_693:hypothetical protein:hypothetical protein:<-->:603641..603958 318 acttcctccataaagatttactctcttgattataccatgaaaaggctacaaatcagcacagcaaactttataattgaaattcaattttttaacatattcactatgacatttttgttttttagtgctatactataggcaataatacatccgagcaaggaggatgttcacatggaagataaataactcattactaatgcaacccaactcttatccgagttaaataaaagtttccaaagctgcaaacagggtactgcagatgatactcgactacaagagctgctaaacactactataaaagagctcaaaaaagcggaaaag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_692:SMT_693|SMT_692:SMT_693:hypothetical protein:hypothetical protein:<-->:603641..603958 318 acttcctccataaagatttactctcttgattataccatgaaaaggctacaaatcagcacagcaaactttataattgaaattcaattttttaacatattcactatgacatttttgttttttagtgctatactataggcaataatacatccgagcaaggaggatgttcacatggaagataaataactcattactaatgcaacccaactcttatccgagttaaataaaagtttccaaagctgcaaacagggtactgcagatgatactcgactacaagagctgctaaacactactataaaagagctcaaaaaagcggaaaag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 1 Min: 142 Max: 318 Len: 177 Subject: UniRef90_Q97QD8 Cluster: Hypothetical protein; n=3; Streptococcus pneumoniae|Rep: Hypothetical protein - Streptococcus pneumoniae HSP 1 e-value: 3.0E-15 bit: 82.8 Len: 177 Query Start:142 Query End:318 Subject Strand: null Subject Start: 8 Subject End: 62 ............................................................................................................................................. I H P S K E D V H M E D K * L I T N A T Q L L S E L N K S F Q S C K Q G T A D D T R L Q E L L N T T I K E L K K A E K ............................................................................................................................................. V H Q I K E D A H M E D K K L I - - - - Q L L S K L N K S Y Q N C K Q G T A D D I R L Q E L L N T T M Q E L K K T E Q acttcctccataaagatttactctcttgattataccatgaaaaggctacaaatcagcacagcaaactttataattgaaattcaattttttaacatattcactatgacatttttgttttttagtgctatactataggcaatannnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn Predict ORF larger than 30AA ================================================ Protein_Len: 41 Strand: + Start: 10 End: 132 ......... M K I Y S L D Y T M K R L Q I S T A N F I I E I Q F F N I F T M T F L F F S A I L .......................................................................................................................................................................................... Protein_Len: 44 Strand: + Start: 187 End: 318 .......................................................................................................................................................................................... M T N A T Q L L S E L N K S F Q S C K Q G T A D D T R L Q E L L N T T I K E L K K A E K Protein_Len: 46 Strand: - Start: 168 End: 305 ....................................................................................................................................................................... M S S L Y S M V L A V W S K D S N F L L K W L Q L C P V A S S V R S C S S S F V V I F S S M ............. acttcctccataaagatttactctcttgattataccatgaaaaggctacaaatcagcacagcaaactttataattgaaattcaattttttaacatattcactatgacatttttgttttttagtgctatactataggcaatannnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn 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: 85 Start: 102 End: 131 .....................................................................................................TATGACATTTTTGTTTTTTAGTGCTATACT........................................................................................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ acttcctccataaagatttactctcttgattataccatgaaaaggctacaaatcagcacagcaaactttataattgaaattcaattttttaacatattcactatgacatttttgttttttagtgctatactataggcaatannnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 73 HP_score: -4.0 Tail_Score: -5.09173 Start: 74 End: 84 Full_Region: CAGCAAACTTTATAA TTGA AAT TCAA TTTTTTAACATATTC .........................................................................TTGAAATTCAA.......................................................................................................................................................................................................................................... Find igs database================================================ Query_seq: SMT_692:SMT_693|SMT_692:SMT_693:hypothetical protein:hypothetical protein:<-->:603641..603958 318 acttcctccataaagatttactctcttgattataccatgaaaaggctacaaatcagcacagcaaactttataattgaaattcaattttttaacatattcactatgacatttttgttttttagtgctatactataggcaatannnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn Intra-Species Hit: Count: 1 Min: 1 Max: 141 Len: 141 Subject: smit_SMT_692_SMT_693|hypothetical protein:hypothetical protein|NEGATIVE:POSITIVE|[603641,603958]|318 HSP 1 e-value: 3.0E-74 bit: 280.0 Len: 141 Query Start:1 Query End:141 Subject Strand: POSITIVE Subject Start: 1 Subject End: 141 acttcctccataaagatttactctcttgattataccatgaaaaggctacaaatcagcacagcaaactttataattgaaattcaattttttaacatattcactatgacatttttgttttttagtgctatactataggcaata................................................................................................................................................................................. acttcctccataaagatttactctcttgattataccatgaaaaggctacaaatcagcacagcaaactttataattgaaattcaattttttaacatattcactatgacatttttgttttttagtgctatactataggcaata................................................................................................................................................................................. Inter-species Hit: Count: 3 Min: 1 Max: 136 Len: 136 Subject: NC_008533_SPD_1136_SPD_1137|Uncharacterized ACR:ABC transporter, ATP-binding protein|NEGATIVE:POSITIVE|[1169744,1170468]|725 HSP 1 e-value: 8.0E-50 bit: 198.0 Len: 136 Query Start:1 Query End:136 Subject Strand: POSITIVE Subject Start: 1 Subject End: 136 acttcctccataaagatttactctcttgattataccatgaaaaggctacaaatcagcacagcaaactttataattgaaattcaattttttaacatattcactatgacatttttgttttttagtgctatactatagg...................................................................................................................................................................................... acttcctccataaagatttactctcttgattataccatgaaaaggctacaaatcagcacaccaaactttgtaattaaaattcaaaattttaacatatttactatgatagttttattttttagtgctatactatagg...................................................................................................................................................................................... Subject: NC_003098_spr1158_spr1159|hypothetical protein:hypothetical protein|NEGATIVE:POSITIVE|[1162213,1162333]|121 HSP 1 e-value: 7.0E-41 bit: 168.0 Len: 121 Query Start:1 Query End:121 Subject Strand: POSITIVE Subject Start: 1 Subject End: 121 acttcctccataaagatttactctcttgattataccatgaaaaggctacaaatcagcacagcaaactttataattgaaattcaattttttaacatattcactatgacatttttgtttttta..................................................................................................................................................................................................... acttcctccataaagatttactctcttgattataccatgaaaaggctacaaatcagcacaccaaactttgtaattaaaattcaaaattttaacatatttactatgatagttttatttttta..................................................................................................................................................................................................... Subject: NC_003028_SP_1280_SP_1281|hypothetical protein:hypothetical protein|NEGATIVE:POSITIVE|[1215603,1215723]|121 HSP 1 e-value: 7.0E-41 bit: 168.0 Len: 121 Query Start:1 Query End:121 Subject Strand: POSITIVE Subject Start: 1 Subject End: 121 acttcctccataaagatttactctcttgattataccatgaaaaggctacaaatcagcacagcaaactttataattgaaattcaattttttaacatattcactatgacatttttgtttttta..................................................................................................................................................................................................... acttcctccataaagatttactctcttgattataccatgaaaaggctacaaatcagcacaccaaactttgtaattaaaattcaaaattttaacatatttactatgatagttttatttttta..................................................................................................................................................................................................... Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACUUCCUCCAUAAAGAUUUACUCUCUUGAUUAUACCAUGAAAAGGCUACAAAUCAGCACAGCAAACUUUAUAAUUGAAAUUCAAUUUUUUAACAUAUUCACUAUGACAUUUUUGUUUUUUAGUGCUAUACUAUAGG ....(((..((((((.(((.((.(.((((((.((((.......)).))..)))))).).)).)))))))))..((((((.......))))))..(((.(((((.((((....))))...)))))..)))....))) (-14.20) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CCUAUAGUAUAGCACUAAAAAACAAAAAUGUCAUAGUGAAUAUGUUAAAAAAUUGAAUUUCAAUUAUAAAGUUUGCUGUGCUGAUUUGUAGCCUUUUCAUGGUAUAAUCAAGAGAGUAAAUCUUUAUGGAGGAAGU ....(((((((.(((((....(((....)))..)))))..))))))).........(((((..((((((((((((((.(..(((((....(((.......)))..)))))..).)))))).))))))))..))))) (-25.20) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 833 70 21 161 112 smit:SMT_692|5end_hypothetical_protein_603550..603780_NEGATIVE 246 73 38 108 74 smit:SMT_149|5end_hypothetical_protein_predicted_by_Glimmer/Critica_98592..98822_POSITIVE 242 48 6 168 121 smit:SMT_1506|5end_Cl-channel,_voltage-gated_family_protein_1489986..1490216_NEGATIVE 228 69 22 130 66 smit:SMT_1497|5end_acetyltransferase,_GNAT_family_1481432..1481662_POSITIVE 226 66 25 63 22 smit:SMT_1208|5end_choline_binding_protein_PcpA_1169690..1169920_NEGATIVE 225 58 13 90 37 smit:SMT_1490|5end_putative_undecaprenyl-phosphate_galactose_phosphotransferase_1470853..1471083_POSITIVE 224 70 21 150 98 smit:SMT_1696|5end_hypothetical_protein_1678182..1678412_POSITIVE 222 48 1 141 95 smit:SMT_1737|5end_peptidyl-prolyl_cis-trans_isomerase_1719862..1720092_POSITIVE 222 65 35 186 158 smit:SMT_1043|5end_chaperonin_GroEL_985766..985996_NEGATIVE 221 63 21 141 95 smit:SMT_745|5end_glycosyl_transferase,_group_1_family_protein_650387..650617_NEGATIVE 217 47 4 68 30 smit:SMT_1294|5end_K02049_sulfonate/nitrate/taurine_transport_system_ATP-binding_protein_1255983..1256213_POSITIVE 216 38 2 109 81 smit:SMT_1503|5end_SSU_ribosomal_protein_S20P_1486900..1487130_POSITIVE 213 80 34 82 32 smit:SMT_243|5end_PTS_system,_mannose-specific_IIC_component_180901..181131_NEGATIVE 211 58 33 110 86 smit:SMT_115|5end_hypothetical_protein_65521..65751_POSITIVE 206 50 2 62 25 smit:SMT_952|5end_hypothetical_protein_900912..901142_NEGATIVE 205 48 2 155 114 smit:SMT_1049|5end_hypothetical_protein_988438..988668_POSITIVE 205 77 31 196 137 smit:SMT_590|5end_tetratricopeptide_repeat_family_protein_506737..506967_POSITIVE 204 50 5 108 58 smit:SMT_2077|5end_chloride_channel_protein_1979429..1979659_NEGATIVE 204 46 4 225 176 smit:SMT_1348|5end_exoribonuclease_II_1327502..1327732_NEGATIVE 204 65 22 58 6 smit:SMT_384|5end_hypothetical_protein_319406..319636_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 257 60 12 133 84 smit:SMT_363|3end_K02519_translation_initiation_factor_IF-2_300751..300901_POSITIVE 246 73 38 37 3 smit:SMT_148|3end_glycoprotein_endopeptidase_98601..98751_POSITIVE 238 129 81 65 17 smit:SMT_1230|3end_hypothetical_protein_1192342..1192492_POSITIVE 228 69 22 140 76 smit:SMT_1496|3end_conserved_hypothetical_protein_TIGR00150_1481522..1481672_POSITIVE 222 48 1 61 15 smit:SMT_1736|3end_acetyltransferase,_GNAT_family_1719862..1720012_POSITIVE 221 63 21 151 105 smit:SMT_746|3end_LPS_biosynthesis_protein_650377..650527_NEGATIVE 217 47 4 68 30 smit:SMT_1293|3end_K02051_sulfonate/nitrate/taurine_transport_system_substrate-binding_protein_1256063..1256213_POSITIVE 216 38 2 56 28 smit:SMT_1502|3end_pantothenate_kinase_1486927..1487077_POSITIVE 211 58 33 38 14 smit:SMT_114|3end_alpha-mannosidase_65529..65679_POSITIVE 208 69 22 122 77 smit:SMT_1439|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1423262..1423412_NEGATIVE 206 50 2 75 38 smit:SMT_953|3end_hypothetical_protein_900899..901049_NEGATIVE 204 46 4 123 74 smit:SMT_1349|3end_K03075_preprotein_translocase_SecG_subunit_1327604..1327754_NEGATIVE 204 63 26 71 23 smit:SMT_481|3end_K03308_neurotransmitter:Na+_symporter,_NSS_family_417641..417791_NEGATIVE 203 49 3 114 61 smit:SMT_1110|3end_hypothetical_protein_1050376..1050526_NEGATIVE 201 67 21 109 58 smit:SMT_1898|3end_aminotransferase_(class_V),_putative_1848877..1849027_NEGATIVE 200 68 21 79 42 smit:SMT_230|3end_hypothetical_protein_predicted_by_Glimmer/Critica_165666..165816_NEGATIVE 199 39 2 44 2 smit:SMT_2171|3end_UDP-N-acetylmuramoylalanyl-D-glutamyl-2,6-_diaminopimelate--D-alanyl-D-alanine_ligase_2043100..2043250_POSITIVE 199 39 2 44 2 smit:SMT_2166|3end_UDP-N-acetylmuramoylalanyl-D-glutamyl-2,6-_diaminopimelate--D-alanyl-D-alanine_ligase_2039912..2040062_POSITIVE 199 39 2 44 2 smit:SMT_1705|3end_UDP-N-acetylmuramoylalanyl-D-glutamyl-2,6-_diaminopimelate--D-alanyl-D-alanine_ligase_1690011..1690161_POSITIVE 198 69 22 85 38 smit:SMT_90|3end_DNA_polymerase_III_beta_subunit_22593..22743_POSITIVE