Origin IGS: tttgaatcctggtcgttaatgaactccccacgaaaataatagatataatattctcatgacaacagctttgcagtgtgtaagaaatgagttagattaaagaattaaaactgtttctcagatgctattttcaaatatgattaataattccttgactacctaatgtagttgaggtatttttgatattattcatatttttgcaaatctattgtttaaaaaataattttctaaaattctgaaaattctgttgacaggactttaaaaagggtctataatggatagaaaaacaaaggagaatact .........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 agtattctcctttgtttttctatccattatagaccctttttaaagtcctgtcaacagaattttcagaattttagaaaattattttttaaacaatagatttgcaaaaatatgaataatatcaaaaatacctcaactacattaggtagtcaaggaattattaatcatatttgaaaatagcatctgagaaacagttttaattctttaatctaactcatttcttacacactgcaaagctgttgtcatgagaatattatatctattattttcgtggggagttcattaacgaccaggattcaaa Mask Tandem Repeat Region ================================================ tttgaatcctggtcgttaatgaactccccacgaaaataatagatataatattctcatgacaacagctttgcagtgtgtaagaaatgagttagattaaagaattaaaactgtttctcagatgctattttcaaatatgattaataattccttgactacctaatgtagttgaggtatttttgatattattcatatttttgcaaatctattgtttaaaaaataattttctaaaattctgaaaattctgttgacaggactttaaaaagggtctataatggatagaaaaacaaaggagaatact Find is-nt database================================================ Query_seq: SMT_296:SMT_297|SMT_296:SMT_297:hypothetical protein predicted by Glimmer/Critica:ABC transporter substrate-binding protein - oligopeptide transport:->->:238389..238686 298 tttgaatcctggtcgttaatgaactccccacgaaaataatagatataatattctcatgacaacagctttgcagtgtgtaagaaatgagttagattaaagaattaaaactgtttctcagatgctattttcaaatatgattaataattccttgactacctaatgtagttgaggtatttttgatattattcatatttttgcaaatctattgtttaaaaaataattttctaaaattctgaaaattctgttgacaggactttaaaaagggtctataatggatagaaaaacaaaggagaatact Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_296:SMT_297|SMT_296:SMT_297:hypothetical protein predicted by Glimmer/Critica:ABC transporter substrate-binding protein - oligopeptide transport:->->:238389..238686 298 tttgaatcctggtcgttaatgaactccccacgaaaataatagatataatattctcatgacaacagctttgcagtgtgtaagaaatgagttagattaaagaattaaaactgtttctcagatgctattttcaaatatgattaataattccttgactacctaatgtagttgaggtatttttgatattattcatatttttgcaaatctattgtttaaaaaataattttctaaaattctgaaaattctgttgacaggactttaaaaagggtctataatggatagaaaaacaaaggagaatact Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_296:SMT_297|SMT_296:SMT_297:hypothetical protein predicted by Glimmer/Critica:ABC transporter substrate-binding protein - oligopeptide transport:->->:238389..238686 298 tttgaatcctggtcgttaatgaactccccacgaaaataatagatataatattctcatgacaacagctttgcagtgtgtaagaaatgagttagattaaagaattaaaactgtttctcagatgctattttcaaatatgattaataattccttgactacctaatgtagttgaggtatttttgatattattcatatttttgcaaatctattgtttaaaaaataattttctaaaattctgaaaattctgttgacaggactttaaaaagggtctataatggatagaaaaacaaaggagaatact Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tttgaatcctggtcgttaatgaactccccacgaaaataatagatataatattctcatgacaacagctttgcagtgtgtaagaaatgagttagattaaagaattaaaactgtttctcagatgctattttcaaatatgattaataattccttgactacctaatgtagttgaggtatttttgatattattcatatttttgcaaatctattgtttaaaaaataattttctaaaattctgaaaattctgttgacaggactttaaaaagggtctataatggatagaaaaacaaaggagaatact Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: - Start: 206 End: 295 ............................................................................................................................................................................................................. Q K F F L K R F N Q F N Q Q C S K L F P R Y H I S F C L L M ... tttgaatcctggtcgttaatgaactccccacgaaaataatagatataatattctcatgacaacagctttgcagtgtgtaagaaatgagttagattaaagaattaaaactgtttctcagatgctattttcaaatatgattaataattccttgactacctaatgtagttgaggtatttttgatattattcatatttttgcaaatctattgtttaaaaaataattttctaaaattctgaaaattctgttgacaggactttaaaaagggtctataatggatagaaaaacaaaggagaatact 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: 89 Start: 244 End: 273 ...................................................................................................................................................................................................................................................GTTGACAGGACTTTAAAAAGGGTCTATAAT......................... PromScan Matrix: RpoD-17 Strand: + Score: 82 Start: 148 End: 177 ...................................................................................................................................................CTTGACTACCTAATGTAGTTGAGGTATTTT......................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tttgaatcctggtcgttaatgaactccccacgaaaataatagatataatattctcatgacaacagctttgcagtgtgtaagaaatgagttagattaaagaattaaaactgtttctcagatgctattttcaaatatgattaataattccttgactacctaatgtagttgaggtatttttgatattattcatatttttgcaaatctattgtttaaaaaataattttctaaaattctgaaaattctgttgacaggactttaaaaagggtctataatggatagaaaaacaaaggagaatact Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 74 HP_score: -4.6 Tail_Score: -4.93316 Start: 145 End: 173 Full_Region: AAATATGATTAATAA TTCCTTGACTAC CTAAT GTAGTTGAGGTA TTTTTGATATTATTC ................................................................................................................................................TTCCTTGACTACCTAATGTAGTTGAGGTA............................................................................................................................. TransTerm Strand: + Conf: 75 HP_score: -7.2 Tail_Score: -4.06487 Start: 147 End: 171 Full_Region: ATATGATTAATAATT CCTTGACTAC CTAAT GTAGTTGAGG TATTTTTGATATTAT ..................................................................................................................................................CCTTGACTACCTAATGTAGTTGAGG............................................................................................................................... Find igs database================================================ Query_seq: SMT_296:SMT_297|SMT_296:SMT_297:hypothetical protein predicted by Glimmer/Critica:ABC transporter substrate-binding protein - oligopeptide transport:->->:238389..238686 298 tttgaatcctggtcgttaatgaactccccacgaaaataatagatataatattctcatgacaacagctttgcagtgtgtaagaaatgagttagattaaagaattaaaactgtttctcagatgctattttcaaatatgattaataattccttgactacctaatgtagttgaggtatttttgatattattcatatttttgcaaatctattgtttaaaaaataattttctaaaattctgaaaattctgttgacaggactttaaaaagggtctataatggatagaaaaacaaaggagaatact Intra-Species Hit: Count: 2 Min: 1 Max: 298 Len: 298 Subject: smit_SMT_296_SMT_297|hypothetical protein predicted by Glimmer/Critica:ABC transporter substrate-binding protein - oligopeptide transport|POSITIVE:POSITIVE|[238389,238686]|298 HSP 1 e-value: 1.0E-168 bit: 591.0 Len: 298 Query Start:1 Query End:298 Subject Strand: POSITIVE Subject Start: 1 Subject End: 298 tttgaatcctggtcgttaatgaactccccacgaaaataatagatataatattctcatgacaacagctttgcagtgtgtaagaaatgagttagattaaagaattaaaactgtttctcagatgctattttcaaatatgattaataattccttgactacctaatgtagttgaggtatttttgatattattcatatttttgcaaatctattgtttaaaaaataattttctaaaattctgaaaattctgttgacaggactttaaaaagggtctataatggatagaaaaacaaaggagaatact tttgaatcctggtcgttaatgaactccccacgaaaataatagatataatattctcatgacaacagctttgcagtgtgtaagaaatgagttagattaaagaattaaaactgtttctcagatgctattttcaaatatgattaataattccttgactacctaatgtagttgaggtatttttgatattattcatatttttgcaaatctattgtttaaaaaataattttctaaaattctgaaaattctgttgacaggactttaaaaagggtctataatggatagaaaaacaaaggagaatact Subject: smit_SMT_293_SMT_294|dTDP-4-dehydrorhamnose reductase:alpha-glucosidase, family 31 of glycosyl hydrolase|POSITIVE:POSITIVE|[236923,237304]|382 HSP 1 e-value: 1.0E-168 bit: 591.0 Len: 298 Query Start:1 Query End:298 Subject Strand: POSITIVE Subject Start: 1 Subject End: 298 tttgaatcctggtcgttaatgaactccccacgaaaataatagatataatattctcatgacaacagctttgcagtgtgtaagaaatgagttagattaaagaattaaaactgtttctcagatgctattttcaaatatgattaataattccttgactacctaatgtagttgaggtatttttgatattattcatatttttgcaaatctattgtttaaaaaataattttctaaaattctgaaaattctgttgacaggactttaaaaagggtctataatggatagaaaaacaaaggagaatact tttgaatcctggtcgttaatgaactccccacgaaaataatagatataatattctcatgacaacagctttgcagtgtgtaagaaatgagttagattaaagaattaaaactgtttctcagatgctattttcaaatatgattaataattccttgactacctaatgtagttgaggtatttttgatattattcatatttttgcaaatctattgtttaaaaaataattttctaaaattctgaaaattctgttgacaggactttaaaaagggtctataatggatagaaaaacaaaggagaatact Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUGAAUCCUGGUCGUUAAUGAACUCCCCACGAAAAUAAUAGAUAUAAUAUUCUCAUGACAACAGCUUUGCAGUGUGUAAGAAAUGAGUUAGAUUAAAGAAUUAAAACUGUUUCUCAGAUGCUAUUUUCAAAUAUGAUUAAUAAUUCCUUGACUACCUAAUGUAGUUGAGGUAUUUUUGAUAUUAUUCAUAUUUUUGCAAAUCUAUUGUUUAAAAAAUAAUUUUCUAAAAUUCUGAAAAUUCUGUUGACAGGACUUUAAAAAGGGUCUAUAAUGGAUAGAAAAACAAAGGAGAAUACU ......((.(((..(((....)))...))).))...............(((((((..(((((.((.((((((((((.(.((((((.((((.((((....))))..)))))))))).).)))).......((((((((.(((((((.(((..(((((.....)))))..))).))......))))).)))))))).)))))).)).)))))..........(((((((.............(((((((...(((((((....))))))).))))))))))))))......))))))).. (-58.81) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGUAUUCUCCUUUGUUUUUCUAUCCAUUAUAGACCCUUUUUAAAGUCCUGUCAACAGAAUUUUCAGAAUUUUAGAAAAUUAUUUUUUAAACAAUAGAUUUGCAAAAAUAUGAAUAAUAUCAAAAAUACCUCAACUACAUUAGGUAGUCAAGGAAUUAUUAAUCAUAUUUGAAAAUAGCAUCUGAGAAACAGUUUUAAUUCUUUAAUCUAACUCAUUUCUUACACACUGCAAAGCUGUUGUCAUGAGAAUAUUAUAUCUAUUAUUUUCGUGGGGAGUUCAUUAACGACCAGGAUUCAAA .......(((((((((......(((...........((((((((((.(((.............))).))))))))))............(((((((.((((((.((((((((.(((((......((.(((..(((((.....)))))..))).))))))).))))))))............(((((((.((((((((....))))...))))..))))))).....)))))).)))))))((((((((((.((....)).)))))))))).))).......)))))..))))...... (-57.94) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 255 278 231 214 171 smit:SMT_1006|5end_6-pyruvoyl_tetrahydrobiopterin_synthase,_putative_946599..946829_POSITIVE 252 178 136 76 37 smit:SMT_310|5end_3-oxoacyl-_251370..251600_POSITIVE 234 45 3 74 24 smit:SMT_131|5end_phosphatase,_putative_83663..83893_NEGATIVE 233 198 157 220 177 smit:SMT_1231|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1192622..1192852_POSITIVE 230 197 153 81 40 smit:SMT_1296|5end_K03696_ATP-dependent_Clp_protease_ATP-binding_subunit_ClpC_1257290..1257520_POSITIVE 230 93 60 52 13 smit:SMT_669|5end_ribose-phosphate_pyrophosphokinase_578160..578390_POSITIVE 227 106 63 230 192 smit:SMT_1123|5end_hypothetical_protein_1059292..1059522_POSITIVE 227 276 231 210 157 smit:SMT_654|5end_K06158_ATP-binding_cassette,_sub-family_F,_member_3_566058..566288_NEGATIVE 225 181 144 64 24 smit:SMT_1152|5end_hypothetical_protein_1097197..1097427_NEGATIVE 223 82 42 41 2 smit:SMT_1008|5end_hypothetical_protein_948021..948251_NEGATIVE 223 286 250 164 113 smit:SMT_668|5end_hypothetical_protein_predicted_by_Glimmer/Critica_578155..578385_NEGATIVE 218 93 51 92 48 smit:SMT_1799|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1773416..1773646_POSITIVE 213 277 232 157 112 smit:SMT_1021|5end_K05846_osmoprotectant_transport_system_permease_protein_957999..958229_NEGATIVE 212 97 56 81 33 smit:SMT_1393|5end_hypothetical_protein_1369106..1369336_POSITIVE 211 45 8 72 33 smit:SMT_1862|5end_K02027_multiple_sugar_transport_system_substrate-binding_protein_1824094..1824324_POSITIVE 211 45 8 72 33 smit:SMT_1763|5end_K02027_multiple_sugar_transport_system_substrate-binding_protein_1738537..1738767_POSITIVE 209 160 116 199 135 smit:SMT_792|5end_hypothetical_protein_predicted_by_Glimmer/Critica_702571..702801_NEGATIVE 208 198 152 192 150 smit:SMT_1756|5end_hypothetical_protein_1734170..1734400_NEGATIVE 206 90 54 96 60 smit:SMT_335|5end_glutamine_synthetase_273753..273983_POSITIVE 205 33 3 121 77 smit:SMT_219|5end_phosphatidate_cytidylyltransferase_150922..151152_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 237 209 168 50 4 smit:SMT_1604|3end_K05833_putative_ABC_transport_system_ATP-binding_protein_1595163..1595313_POSITIVE 234 45 3 52 2 smit:SMT_132|3end_L-serine_dehydratase_alpha_subunit_83685..83835_NEGATIVE 230 197 153 79 38 smit:SMT_1295|3end_transcriptional_regulator_CtsR_1257368..1257518_POSITIVE 220 90 54 118 80 smit:SMT_2002|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1924145..1924295_NEGATIVE 217 93 54 142 96 smit:SMT_326|3end_K02029_polar_amino_acid_transport_system_permease_protein_263217..263367_NEGATIVE 214 94 54 121 80 smit:SMT_1927|3end_cell_division_protein_FtsH_1868408..1868558_NEGATIVE 214 96 55 145 109 smit:SMT_1801|3end_heavy_metal_translocating_P-type_ATPase_1775408..1775558_POSITIVE 212 97 56 81 33 smit:SMT_1392|3end_dihydroxyacetone_kinase_1369186..1369336_POSITIVE 211 188 147 91 58 smit:SMT_1419|3end_hypothetical_protein_1404582..1404732_POSITIVE 210 83 59 144 113 smit:SMT_1039|3end_tRNA_(uracil-5-)_-methyltransferase_981343..981493_NEGATIVE 207 92 54 57 19 smit:SMT_1895|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1847402..1847552_POSITIVE 206 90 54 59 23 smit:SMT_334|3end_K03713_MerR_family_transcriptional_regulator,_glutamine_synthetase_repressor_273796..273946_POSITIVE 205 35 8 136 113 smit:SMT_1690|3end_K06148_ATP-binding_cassette,_subfamily_C,_bacterial_1673370..1673520_NEGATIVE 205 33 3 112 68 smit:SMT_218|3end_undecaprenyl_pyrophosphate_synthetase_150993..151143_POSITIVE 203 100 56 151 105 smit:SMT_2044|3end_transcriptional_activator_TipA,_putative_1955274..1955424_NEGATIVE 203 76 53 40 17 smit:SMT_1383|3end_ribonucleoside-diphosphate_reductase_alpha_chain_1360795..1360945_NEGATIVE 203 149 110 142 111 smit:SMT_289|3end_glycosyltransferase_233328..233478_POSITIVE 202 99 54 73 23 smit:SMT_2030|3end_chromosomal_replication_initiator_protein_DnaA_1944790..1944940_NEGATIVE 201 106 64 45 7 smit:SMT_508|3end_hypothetical_protein_438477..438627_NEGATIVE 201 178 147 32 1 smit:SMT_309|3end_acyl-carrier-protein_S-malonyltransferase_251406..251556_POSITIVE