Origin IGS: gatcaattgatttcgtgtattcattcctaattcctaaaaattgaatcactgttttcctcaggtctatctgggggaggcagtgattttttgaaacgaaagcatagatatccgtgttttcttatcactatttaaccattcaggaaatcttaagtaccatttaggatttggagtaaggatttaggaaattatggcttatattagagatgttccaagtttacaaaggagggttcac .........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 gtgaaccctcctttgtaaacttggaacatctctaatataagccataatttcctaaatccttactccaaatcctaaatggtacttaagatttcctgaatggttaaatagtgataagaaaacacggatatctatgctttcgtttcaaaaaatcactgcctcccccagatagacctgaggaaaacagtgattcaatttttaggaattaggaatgaatacacgaaatcaattgatc Mask Tandem Repeat Region ================================================ gatcaattgatttcgtgtattcattcctaattcctaaaaattgaatcactgttttcctcaggtctatctgggggaggcagtgattttttgaaacgaaagcatagatatccgtgttttcttatcactatttaaccattcaggaaatcttaagtaccatttaggatttggagtaaggatttaggaaattatggcttatattagagatgttccaagtttacaaaggagggttcac Find is-nt database================================================ Query_seq: SMT_119:SMT_120|SMT_119:SMT_120:K02027 multiple sugar transport system substrate-binding protein:hypothetical protein:->->:72082..72313 232 gatcaattgatttcgtgtattcattcctaattcctaaaaattgaatcactgttttcctcaggtctatctgggggaggcagtgattttttgaaacgaaagcatagatatccgtgttttcttatcactatttaaccattcaggaaatcttaagtaccatttaggatttggagtaaggatttaggaaattatggcttatattagagatgttccaagtttacaaaggagggttcac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_119:SMT_120|SMT_119:SMT_120:K02027 multiple sugar transport system substrate-binding protein:hypothetical protein:->->:72082..72313 232 gatcaattgatttcgtgtattcattcctaattcctaaaaattgaatcactgttttcctcaggtctatctgggggaggcagtgattttttgaaacgaaagcatagatatccgtgttttcttatcactatttaaccattcaggaaatcttaagtaccatttaggatttggagtaaggatttaggaaattatggcttatattagagatgttccaagtttacaaaggagggttcac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_119:SMT_120|SMT_119:SMT_120:K02027 multiple sugar transport system substrate-binding protein:hypothetical protein:->->:72082..72313 232 gatcaattgatttcgtgtattcattcctaattcctaaaaattgaatcactgttttcctcaggtctatctgggggaggcagtgattttttgaaacgaaagcatagatatccgtgttttcttatcactatttaaccattcaggaaatcttaagtaccatttaggatttggagtaaggatttaggaaattatggcttatattagagatgttccaagtttacaaaggagggttcac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gatcaattgatttcgtgtattcattcctaattcctaaaaattgaatcactgttttcctcaggtctatctgggggaggcagtgattttttgaaacgaaagcatagatatccgtgttttcttatcactatttaaccattcaggaaatcttaagtaccatttaggatttggagtaaggatttaggaaattatggcttatattagagatgttccaagtttacaaaggagggttcac Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: + Start: 40 End: 129 ....................................... M E S L F S S G L S G G G S D F L K R K H R Y P C F L I T I ....................................................................................................... Protein_Len: 37 Strand: - Start: 67 End: 177 .................................................................. R P S A T I K Q F S L M S I R T K K D S N L W E P F R L Y W K P N P T L M ....................................................... Protein_Len: 33 Strand: - Start: 30 End: 128 ............................. N R F I S D S N E E P R D P P P L S K K F R F C L Y G H K R I V M ........................................................................................................ Protein_Len: 35 Strand: - Start: 2 End: 106 . D I S K T Y E N R I G L F Q I V T K R L D I Q P L C H N K S V F A Y M .............................................................................................................................. gatcaattgatttcgtgtattcattcctaattcctaaaaattgaatcactgttttcctcaggtctatctgggggaggcagtgattttttgaaacgaaagcatagatatccgtgttttcttatcactatttaaccattcaggaaatcttaagtaccatttaggatttggagtaaggatttaggaaattatggcttatattagagatgttccaagtttacaaaggagggttcac Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ gatcaattgatttcgtgtattcattcctaattcctaaaaattgaatcactgttttcctcaggtctatctgggggaggcagtgattttttgaaacgaaagcatagatatccgtgttttcttatcactatttaaccattcaggaaatcttaagtaccatttaggatttggagtaaggatttaggaaattatggcttatattagagatgttccaagtttacaaaggagggttcac Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 100 HP_score: -12.1 Tail_Score: -5.00616 Start: 46 End: 83 Full_Region: TTCCTAAAAATTGAA TCACTGTTTTCCTCAGG TCTA TCTGGGGGAGGCAGTGA TTTTTTGAAACGAAA .............................................TCACTGTTTTCCTCAGGTCTATCTGGGGGAGGCAGTGA..................................................................................................................................................... TransTerm Strand: - Conf: 47 HP_score: -2.6 Tail_Score: -3.45031 Start: 46 End: 83 Full_Region: tttcgtttcaaaaaa tcactgcctcccccag atagac ctgaggaaaacagtga ttcaatttttaggaa .............................................tcactgcctcccccagatagacctgaggaaaacagtga..................................................................................................................................................... Find igs database================================================ Query_seq: SMT_119:SMT_120|SMT_119:SMT_120:K02027 multiple sugar transport system substrate-binding protein:hypothetical protein:->->:72082..72313 232 gatcaattgatttcgtgtattcattcctaattcctaaaaattgaatcactgttttcctcaggtctatctgggggaggcagtgattttttgaaacgaaagcatagatatccgtgttttcttatcactatttaaccattcaggaaatcttaagtaccatttaggatttggagtaaggatttaggaaattatggcttatattagagatgttccaagtttacaaaggagggttcac Intra-Species Hit: Count: 1 Min: 1 Max: 232 Len: 232 Subject: smit_SMT_119_SMT_120|K02027 multiple sugar transport system substrate-binding protein:hypothetical protein|POSITIVE:POSITIVE|[72082,72313]|232 HSP 1 e-value: 1.0E-128 bit: 460.0 Len: 232 Query Start:1 Query End:232 Subject Strand: POSITIVE Subject Start: 1 Subject End: 232 gatcaattgatttcgtgtattcattcctaattcctaaaaattgaatcactgttttcctcaggtctatctgggggaggcagtgattttttgaaacgaaagcatagatatccgtgttttcttatcactatttaaccattcaggaaatcttaagtaccatttaggatttggagtaaggatttaggaaattatggcttatattagagatgttccaagtttacaaaggagggttcac gatcaattgatttcgtgtattcattcctaattcctaaaaattgaatcactgttttcctcaggtctatctgggggaggcagtgattttttgaaacgaaagcatagatatccgtgttttcttatcactatttaaccattcaggaaatcttaagtaccatttaggatttggagtaaggatttaggaaattatggcttatattagagatgttccaagtttacaaaggagggttcac Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAUCAAUUGAUUUCGUGUAUUCAUUCCUAAUUCCUAAAAAUUGAAUCACUGUUUUCCUCAGGUCUAUCUGGGGGAGGCAGUGAUUUUUUGAAACGAAAGCAUAGAUAUCCGUGUUUUCUUAUCACUAUUUAACCAUUCAGGAAAUCUUAAGUACCAUUUAGGAUUUGGAGUAAGGAUUUAGGAAAUUAUGGCUUAUAUUAGAGAUGUUCCAAGUUUACAAAGGAGGGUUCAC .......(((.(((.((((..(.(((((((.((((.......((((((((((((((((((((....))))))))))))))))))))..(((...(((((((..(....)..)))))))...)))..........((((...(((((((((((...))))))))))).)))).)))).)))))))....(((..(((.......)))..))).)..)))).....))).))). (-64.90) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUGAACCCUCCUUUGUAAACUUGGAACAUCUCUAAUAUAAGCCAUAAUUUCCUAAAUCCUUACUCCAAAUCCUAAAUGGUACUUAAGAUUUCCUGAAUGGUUAAAUAGUGAUAAGAAAACACGGAUAUCUAUGCUUUCGUUUCAAAAAAUCACUGCCUCCCCCAGAUAGACCUGAGGAAAACAGUGAUUCAAUUUUUAGGAAUUAGGAAUGAAUACACGAAAUCAAUUGAUC (((........((((((...(((((.....))))))))))).......(((((((...((((..(((.........)))....))))..((((((((...........(((...((((.((..(....)..)).))))...)))...((((((((..(((..(((......))).)))...)))))))).....)))))))))))))))......))).............. (-42.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 292 97 53 51 4 smit:SMT_1059|5end_NAD(P)H-flavin_oxidoreductase_997379..997609_POSITIVE 286 78 45 58 14 smit:SMT_952|5end_hypothetical_protein_900912..901142_NEGATIVE 279 107 63 68 8 smit:SMT_876|5end_hypothetical_protein_predicted_by_Glimmer/Critica_823502..823732_NEGATIVE 279 107 63 186 126 smit:SMT_875|5end_nitroreductase_family_protein_823384..823614_NEGATIVE 277 91 54 48 11 smit:SMT_1010|5end_hypothetical_protein_948292..948522_POSITIVE 271 96 55 84 46 smit:SMT_1602|5end_hypothetical_protein_1592385..1592615_POSITIVE 271 100 52 170 121 smit:SMT_1585|5end_phosphopantetheine_adenylyltransferase_1575242..1575472_POSITIVE 266 90 48 130 92 smit:SMT_422|5end_K02004_363781..364011_POSITIVE 265 110 67 208 163 smit:SMT_124|5end_hypothetical_protein_76654..76884_NEGATIVE 261 78 31 215 151 smit:SMT_563|5end_thioredoxin_reductase_480988..481218_POSITIVE 258 105 71 195 149 smit:SMT_2028|5end_leader_peptidase_(prepilin_peptidase)_/_N-methyltransferase_1943729..1943959_NEGATIVE 258 105 71 195 149 smit:SMT_1754|5end_leader_peptidase_(prepilin_peptidase)_/_N-methyltransferase_1733022..1733252_NEGATIVE 256 69 21 63 15 smit:SMT_1519|5end_DNA-binding_response_regulator_VncR_1499662..1499892_NEGATIVE 255 79 31 226 173 smit:SMT_1346|5end_tellurite_resistance_protein_TehB_1324703..1324933_NEGATIVE 254 168 121 142 92 smit:SMT_2045|5end_K+_transport_system,_NAD-binding_component_1956139..1956369_POSITIVE 254 81 42 120 80 smit:SMT_1122|5end_queuine_tRNA-ribosyltransferase_1059223..1059453_NEGATIVE 254 79 50 53 20 smit:SMT_998|5end_peptide_chain_release_factor_3_941243..941473_NEGATIVE 254 90 44 137 86 smit:SMT_894|5end_hypothetical_protein_841701..841931_NEGATIVE 253 120 71 104 64 smit:SMT_207|5end_putative_two-component_sensor_histidine_kinase_139879..140109_NEGATIVE 252 117 71 181 146 smit:SMT_298|5end_penicillin-binding_protein_1A_242902..243132_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 495 85 44 47 2 smit:SMT_119|3end_K02027_multiple_sugar_transport_system_substrate-binding_protein_72021..72171_POSITIVE 292 97 53 54 7 smit:SMT_1058|3end_primosomal_protein_DnaI_997462..997612_POSITIVE 286 78 45 71 27 smit:SMT_953|3end_hypothetical_protein_900899..901049_NEGATIVE 266 90 48 117 79 smit:SMT_421|3end_K02003_363848..363998_POSITIVE 265 110 67 145 100 smit:SMT_125|3end_hypothetical_protein_76717..76867_NEGATIVE 255 91 56 36 1 smit:SMT_1009|3end_hypothetical_protein_predicted_by_Glimmer/Critica_948360..948510_POSITIVE 254 90 44 144 93 smit:SMT_895|3end_cysteinyl-tRNA_synthetase_841694..841844_NEGATIVE 252 109 61 92 49 smit:SMT_1070|3end_hypothetical_protein_1009644..1009794_NEGATIVE 250 100 59 148 86 smit:SMT_1819|3end_K03442_small_conductance_mechanosensitive_ion_channel,_MscS_family_1793555..1793705_POSITIVE 250 78 31 136 94 smit:SMT_1265|3end_hypothetical_protein_1230872..1231022_NEGATIVE 249 109 61 65 14 smit:SMT_2163|3end_cell_division_protein_FtsA_2037917..2038067_POSITIVE 248 60 11 63 19 smit:SMT_1593|3end_ABC-type_oligopeptide_transport_system,_periplasmic_component_1583485..1583635_POSITIVE 246 100 60 53 8 smit:SMT_763|3end_alpha-amylase_669280..669430_POSITIVE 244 89 42 54 7 smit:SMT_692|3end_hypothetical_protein_603008..603158_NEGATIVE 241 96 54 56 16 smit:SMT_228|3end_hypothetical_protein_165093..165243_POSITIVE 241 96 54 56 16 smit:SMT_224|3end_hypothetical_protein_159599..159749_POSITIVE 240 62 32 133 102 smit:SMT_1551|3end_K02221_YggT_family_protein_1535202..1535352_POSITIVE 236 92 53 55 18 smit:SMT_972|3end_ABC-type_multidrug/protein/lipid_transport_system,_ATPase_component_919256..919406_NEGATIVE 236 75 31 59 13 smit:SMT_593|3end_K02030_polar_amino_acid_transport_system_substrate-binding_protein_510317..510467_POSITIVE 236 83 42 84 37 smit:SMT_363|3end_K02519_translation_initiation_factor_IF-2_300751..300901_POSITIVE