Origin IGS: ttcaattatcccagaactgataacaaatatcatggcttgtttaaaacaaccatgatatttttgtttttgttttcttttgttttttaaattgattgattgaatactttatgataaaatagtaatagaaatagaggtgataacg .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 cgttatcacctctatttctattactattttatcataaagtattcaatcaatcaatttaaaaaacaaaagaaaacaaaaacaaaaatatcatggttgttttaaacaagccatgatatttgttatcagttctgggataattgaa Mask Tandem Repeat Region ================================================ ttcaattatcccagaactgataacaaatatcatggcttgtttaaaacaaccatgatatttttgtttttgttttcttttgttttttaaattgattgattgaatactttatgataaaatagtaatagaaatagaggtgataacg Find is-nt database================================================ Query_seq: SMT_636:SMT_637|SMT_636:SMT_637:ribonucleoside-diphosphate reductase beta chain:lactose phosphotransferase system repressor:->->:542256..542397 142 ttcaattatcccagaactgataacaaatatcatggcttgtttaaaacaaccatgatatttttgtttttgttttcttttgttttttaaattgattgattgaatactttatgataaaatagtaatagaaatagaggtgataacg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_636:SMT_637|SMT_636:SMT_637:ribonucleoside-diphosphate reductase beta chain:lactose phosphotransferase system repressor:->->:542256..542397 142 ttcaattatcccagaactgataacaaatatcatggcttgtttaaaacaaccatgatatttttgtttttgttttcttttgttttttaaattgattgattgaatactttatgataaaatagtaatagaaatagaggtgataacg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_636:SMT_637|SMT_636:SMT_637:ribonucleoside-diphosphate reductase beta chain:lactose phosphotransferase system repressor:->->:542256..542397 142 ttcaattatcccagaactgataacaaatatcatggcttgtttaaaacaaccatgatatttttgtttttgttttcttttgttttttaaattgattgattgaatactttatgataaaatagtaatagaaatagaggtgataacg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttcaattatcccagaactgataacaaatatcatggcttgtttaaaacaaccatgatatttttgtttttgttttcttttgttttttaaattgattgattgaatactttatgataaaatagtaatagaaatagaggtgataacg Predict ORF larger than 30AA ================================================ Protein_Len: 34 Strand: - Start: 1 End: 102 E I I G S S I V F I M A Q K F C G H Y K Q K Q K R K N K L N I S Q M ........................................ ttcaattatcccagaactgataacaaatatcatggcttgtttaaaacaaccatgatatttttgtttttgttttcttttgttttttaaattgattgattgaatactttatgataaaatagtaatagaaatagaggtgataacg 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: 86 Start: 88 End: 117 .......................................................................................ATTGATTGATTGAATACTTTATGATAAAAT......................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ ttcaattatcccagaactgataacaaatatcatggcttgtttaaaacaaccatgatatttttgtttttgttttcttttgttttttaaattgattgattgaatactttatgataaaatagtaatagaaatagaggtgataacg Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 41 HP_score: -2.9 Tail_Score: -2.60688 Start: 18 End: 32 Full_Region: gttttaaacaagcca tgata tttgt tatca gttctgggataattg .................tgatatttgttatca.............................................................................................................. TransTerm Strand: + Conf: 100 HP_score: -7.5 Tail_Score: -5.70761 Start: 21 End: 63 Full_Region: TTATCCCAGAACTGA TAACAAATATCATGGCTTGTT TAA AACAACCATGATATTTTTG TTTTTGTTTTCTTTT ....................TAACAAATATCATGGCTTGTTTAAAACAACCATGATATTTTTG............................................................................... TransTerm Strand: - Conf: 89 HP_score: -10.3 Tail_Score: -4.36206 Start: 28 End: 57 Full_Region: aaacaaaaacaaaaa tatcatggttgtt tta aacaagccatgata tttgttatcagttct ...........................tatcatggttgttttaaacaagccatgata..................................................................................... Find igs database================================================ Query_seq: SMT_636:SMT_637|SMT_636:SMT_637:ribonucleoside-diphosphate reductase beta chain:lactose phosphotransferase system repressor:->->:542256..542397 142 ttcaattatcccagaactgataacaaatatcatggcttgtttaaaacaaccatgatatttttgtttttgttttcttttgttttttaaattgattgattgaatactttatgataaaatagtaatagaaatagaggtgataacg Intra-Species Hit: Count: 1 Min: 1 Max: 142 Len: 142 Subject: smit_SMT_636_SMT_637|ribonucleoside-diphosphate reductase beta chain:lactose phosphotransferase system repressor|POSITIVE:POSITIVE|[542256,542397]|142 HSP 1 e-value: 2.0E-24 bit: 113.0 Len: 57 Query Start:1 Query End:57 Subject Strand: POSITIVE Subject Start: 1 Subject End: 57 ttcaattatcccagaactgataacaaatatcatggcttgtttaaaacaaccatgata..................................................................................... ttcaattatcccagaactgataacaaatatcatggcttgtttaaaacaaccatgata..................................................................................... HSP 2 e-value: 2.0E-24 bit: 113.0 Len: 57 Query Start:86 Query End:142 Subject Strand: POSITIVE Subject Start: 86 Subject End: 142 .....................................................................................aaattgattgattgaatactttatgataaaatagtaatagaaatagaggtgataacg .....................................................................................aaattgattgattgaatactttatgataaaatagtaatagaaatagaggtgataacg Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUCAAUUAUCCCAGAACUGAUAACAAAUAUCAUGGCUUGUUUAAAACAACCAUGAUAUUUUUGUUUUUGUUUUCUUUUGUUUUUUAAAUUGAUUGAUUGAAUACUUUAUGAUAAAAUAGUAAUAGAAAUAGAGGUGAUAACG .....(((((((............(((((((((((.((((.....)))))))))))))))(((((((((((...(((((((...((((...(((.....)))..)))).)))))))....))))))))))).)).))))).. (-28.50) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CGUUAUCACCUCUAUUUCUAUUACUAUUUUAUCAUAAAGUAUUCAAUCAAUCAAUUUAAAAAACAAAAGAAAACAAAAACAAAAAUAUCAUGGUUGUUUUAAACAAGCCAUGAUAUUUGUUAUCAGUUCUGGGAUAAUUGAA .((((((.((..............(((((((...)))))))..........................((((......(((((..(((((((((((((.....)).)))))))))))))))).....)))))))))))).... (-23.70) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 226 42 9 135 97 smit:SMT_2023|5end_tryptophan_synthase,_alpha_subunit_1939315..1939545_POSITIVE 226 42 9 135 97 smit:SMT_1818|5end_tryptophan_synthase,_alpha_subunit_1792190..1792420_POSITIVE 218 41 15 144 117 smit:SMT_727|5end_phage_transcriptional_repressor_632513..632743_NEGATIVE 217 100 51 156 108 smit:SMT_1391|5end_dihydroxyacetone_kinase_1367520..1367750_POSITIVE 213 110 62 139 91 smit:SMT_449|5end_hypothetical_protein_387615..387845_POSITIVE 207 45 1 77 38 smit:SMT_802|5end_aldo/keto_reductase_family_712328..712558_NEGATIVE 206 40 8 168 129 smit:SMT_549|5end_hypothetical_cytosolic_protein_467057..467287_POSITIVE 205 38 1 88 56 smit:SMT_1191|5end_phosphoribosylamine--glycine_ligase_1149737..1149967_NEGATIVE 204 61 32 202 166 smit:SMT_1585|5end_phosphopantetheine_adenylyltransferase_1575242..1575472_POSITIVE 196 38 2 88 57 smit:SMT_2076|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1978592..1978822_NEGATIVE 196 38 2 195 164 smit:SMT_2075|5end_phosphoribosylamine--glycine_ligase_1978485..1978715_NEGATIVE 196 95 64 231 203 smit:SMT_431|5end_UDP-N-acetylmuramoyl-L-alanyl-D-glutamate_synthetase_372199..372429_POSITIVE 193 97 53 182 138 smit:SMT_1539|5end_sensor_histidine_kinase,_putative_1524310..1524540_NEGATIVE 190 87 43 119 59 smit:SMT_1783|5end_peptide_methionine_sulfoxide_reductase_1759756..1759986_POSITIVE 188 78 33 59 10 smit:SMT_942|5end_hypothetical_protein_894067..894297_NEGATIVE 186 137 96 196 152 smit:SMT_1583|5end_polysaccharide_transporter,_PST_family_1573963..1574193_POSITIVE 186 137 96 196 152 smit:SMT_286|5end_polysaccharide_transporter,_PST_family_228655..228885_POSITIVE 185 99 52 127 85 smit:SMT_1768|5end_hydrolase,_alpha/beta_fold_family_1744959..1745189_NEGATIVE 184 85 52 53 21 smit:SMT_359|5end_transcription_termination-antitermination_factor_294470..294700_POSITIVE 182 60 11 98 45 smit:SMT_1092|5end_transcription_antitermination_factor_1033696..1033926_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 338 69 22 79 26 smit:SMT_636|3end_ribonucleoside-diphosphate_reductase_beta_chain_542195..542345_POSITIVE 225 68 23 48 4 smit:SMT_1829|3end_hypothetical_protein_1799132..1799282_POSITIVE 216 100 64 122 88 smit:SMT_430|3end_hypothetical_protein_372164..372314_POSITIVE 213 110 62 134 86 smit:SMT_448|3end_K03707_transcriptional_activator_TenA_387690..387840_POSITIVE 206 40 8 70 31 smit:SMT_548|3end_K02035_peptide/nickel_transport_system_substrate-binding_protein_467039..467189_POSITIVE 190 84 43 53 10 smit:SMT_273|3end_glucan_1,6-alpha-glucosidase_215105..215255_POSITIVE 190 77 33 70 19 smit:SMT_184|3end_30S_ribosomal_protein_S8_121891..122041_POSITIVE 187 40 10 126 102 smit:SMT_1909|3end_zinc_metalloprotease_ZmpB,_truncated_1855295..1855445_NEGATIVE 187 93 58 121 88 smit:SMT_1804|3end_hypothetical_protein_1780314..1780464_POSITIVE 185 99 52 113 71 smit:SMT_1769|3end_alcohol_dehydrogenase,_zinc-containing_1744973..1745123_NEGATIVE 182 138 91 55 5 smit:SMT_1747|3end_anthranilate_synthase_component_I_1726832..1726982_POSITIVE 180 88 53 102 68 smit:SMT_1311|3end_integral_membrane_protein_1277108..1277258_POSITIVE 178 140 109 39 3 smit:SMT_1618|3end_K02015_iron_complex_transport_system_permease_protein_1604490..1604640_NEGATIVE 177 75 31 151 109 smit:SMT_1983|3end_glycerophosphoryl_diester_phosphodiesterase_1913455..1913605_NEGATIVE 177 86 46 93 47 smit:SMT_1315|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1280952..1281102_POSITIVE 176 85 54 85 56 smit:SMT_1400|3end_acetoin_dehydrogenase_complex,_E1_component,_alpha_subunit_1377077..1377227_POSITIVE 175 85 48 65 11 smit:SMT_309|3end_acyl-carrier-protein_S-malonyltransferase_251406..251556_POSITIVE 174 37 6 118 91 smit:SMT_1604|3end_K05833_putative_ABC_transport_system_ATP-binding_protein_1595163..1595313_POSITIVE 173 100 52 94 51 smit:SMT_865|3end_50S_ribosomal_protein_L1_815022..815172_NEGATIVE 172 44 9 76 33 smit:SMT_143|3end_hypothetical_protein_95090..95240_NEGATIVE