Origin IGS: ttgtcatttattccttctttttcatagattaacagatcagggctctgtcaggccgctactacctcgcgtaggagattgaactgcctacattcttctgcactgacgataggctttcaccccctttccatgacatagcagcagcttttcaactacagcttc .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gaagctgtagttgaaaagctgctgctatgtcatggaaagggggtgaaagcctatcgtcagtgcagaagaatgtaggcagttcaatctcctacgcgaggtagtagcggcctgacagagccctgatctgttaatctatgaaaaagaaggaataaatgacaa Mask Tandem Repeat Region ================================================ ttgtcatttattccttctttttcatagattaacagatcagggctctgtcaggccgctactacctcgcgtaggagattgaactgcctacattcttctgcactgacgataggctttcaccccctttccatgacatagcagcagcttttcaactacagcttc Find is-nt database================================================ Query_seq: SMT_772:SMT_773|SMT_772:SMT_773:spermidine/putrescine ABC transporter, ATP-binding protein:UDP-N-acetylenolpyruvoylglucosamine reductase:<-<-:683391..683549 159 ttgtcatttattccttctttttcatagattaacagatcagggctctgtcaggccgctactacctcgcgtaggagattgaactgcctacattcttctgcactgacgataggctttcaccccctttccatgacatagcagcagcttttcaactacagcttc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_772:SMT_773|SMT_772:SMT_773:spermidine/putrescine ABC transporter, ATP-binding protein:UDP-N-acetylenolpyruvoylglucosamine reductase:<-<-:683391..683549 159 ttgtcatttattccttctttttcatagattaacagatcagggctctgtcaggccgctactacctcgcgtaggagattgaactgcctacattcttctgcactgacgataggctttcaccccctttccatgacatagcagcagcttttcaactacagcttc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_772:SMT_773|SMT_772:SMT_773:spermidine/putrescine ABC transporter, ATP-binding protein:UDP-N-acetylenolpyruvoylglucosamine reductase:<-<-:683391..683549 159 ttgtcatttattccttctttttcatagattaacagatcagggctctgtcaggccgctactacctcgcgtaggagattgaactgcctacattcttctgcactgacgataggctttcaccccctttccatgacatagcagcagcttttcaactacagcttc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttgtcatttattccttctttttcatagattaacagatcagggctctgtcaggccgctactacctcgcgtaggagattgaactgcctacattcttctgcactgacgataggctttcaccccctttccatgacatagcagcagcttttcaactacagcttc Predict ORF larger than 30AA ================================================ Protein_Len: 35 Strand: + Start: 28 End: 132 ........................... M N R S G L C Q A A T T S R R R L N C L H S S A L T I G F H P L S M T ........................... ttgtcatttattccttctttttcatagattaacagatcagggctctgtcaggccgctactacctcgcgtaggagattgaactgcctacattcttctgcactgacgataggctttcaccccctttccatgacatagcagcagcttttcaactacagcttc 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================================================ ttgtcatttattccttctttttcatagattaacagatcagggctctgtcaggccgctactacctcgcgtaggagattgaactgcctacattcttctgcactgacgataggctttcaccccctttccatgacatagcagcagcttttcaactacagcttc Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_772:SMT_773|SMT_772:SMT_773:spermidine/putrescine ABC transporter, ATP-binding protein:UDP-N-acetylenolpyruvoylglucosamine reductase:<-<-:683391..683549 159 ttgtcatttattccttctttttcatagattaacagatcagggctctgtcaggccgctactacctcgcgtaggagattgaactgcctacattcttctgcactgacgataggctttcaccccctttccatgacatagcagcagcttttcaactacagcttc Intra-Species Hit: Count: 1 Min: 1 Max: 159 Len: 159 Subject: smit_SMT_772_SMT_773|spermidine/putrescine ABC transporter, ATP-binding protein:UDP-N-acetylenolpyruvoylglucosamine reductase|NEGATIVE:NEGATIVE|[683391,683549]|159 HSP 1 e-value: 2.0E-85 bit: 315.0 Len: 159 Query Start:1 Query End:159 Subject Strand: POSITIVE Subject Start: 1 Subject End: 159 ttgtcatttattccttctttttcatagattaacagatcagggctctgtcaggccgctactacctcgcgtaggagattgaactgcctacattcttctgcactgacgataggctttcaccccctttccatgacatagcagcagcttttcaactacagcttc ttgtcatttattccttctttttcatagattaacagatcagggctctgtcaggccgctactacctcgcgtaggagattgaactgcctacattcttctgcactgacgataggctttcaccccctttccatgacatagcagcagcttttcaactacagcttc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUGUCAUUUAUUCCUUCUUUUUCAUAGAUUAACAGAUCAGGGCUCUGUCAGGCCGCUACUACCUCGCGUAGGAGAUUGAACUGCCUACAUUCUUCUGCACUGACGAUAGGCUUUCACCCCCUUUCCAUGACAUAGCAGCAGCUUUUCAACUACAGCUUC ..........................((((....)))).(((((.((..((((.(((.(((..(((.(.(((.(..((((..(((((...((.((......)).))))))).))))..))))...).)))..))).))).))))..)).....))))). (-29.10) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAAGCUGUAGUUGAAAAGCUGCUGCUAUGUCAUGGAAAGGGGGUGAAAGCCUAUCGUCAGUGCAGAAGAAUGUAGGCAGUUCAAUCUCCUACGCGAGGUAGUAGCGGCCUGACAGAGCCCUGAUCUGUUAAUCUAUGAAAAAGAAGGAAUAAAUGACAA ......((((.......(((((((((((.((.((...((((((((((.((((((..((.........))..))))))..))).))))))).)).)).))))))))))).(((((((.......)))))))..))))....................... (-48.30) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 1073 90 41 181 132 smit:SMT_772|5end_spermidine/putrescine_ABC_transporter,_ATP-binding_protein_683300..683530_NEGATIVE 378 90 43 157 96 smit:SMT_2067|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1973432..1973662_POSITIVE 357 144 104 213 169 smit:SMT_2002|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1924405..1924635_NEGATIVE 357 144 104 213 169 smit:SMT_1942|5end_zinc_metalloprotease_ZmpB,_truncated_1877882..1878112_POSITIVE 351 80 33 206 165 smit:SMT_2051|5end_enoyl-CoA_hydratase_1960639..1960869_NEGATIVE 344 147 108 184 141 smit:SMT_1114|5end_competence_protein_1052555..1052785_NEGATIVE 327 87 41 112 50 smit:SMT_1953|5end_hypothetical_protein_1886897..1887127_POSITIVE 322 120 71 101 57 smit:SMT_556|5end_putative_aminotransferase_473544..473774_POSITIVE 318 136 93 218 171 smit:SMT_1358|5end_dihydroorotate_dehydrogenase_B_1337192..1337422_NEGATIVE 317 129 85 123 54 smit:SMT_1235|5end_transcriptional_regulator,_MerR_family_1195539..1195769_POSITIVE 313 98 51 67 1 smit:SMT_1373|5end_K02838_ribosome_recycling_factor_1352274..1352504_NEGATIVE 307 79 33 140 104 smit:SMT_1993|5end_hypothetical_protein_1919800..1920030_NEGATIVE 307 150 119 168 143 smit:SMT_382|5end_valyl-tRNA_synthetase_317706..317936_POSITIVE 306 66 39 50 27 smit:SMT_1668|5end_K+_transport_system,_NAD-binding_component_1658288..1658518_NEGATIVE 303 129 84 196 146 smit:SMT_1328|5end_hypothetical_protein_1304468..1304698_NEGATIVE 303 109 61 78 24 smit:SMT_1268|5end_acetoin_reductase_1233419..1233649_NEGATIVE 300 140 93 230 176 smit:SMT_1885|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1840057..1840287_NEGATIVE 298 99 51 136 95 smit:SMT_941|5end_hypothetical_protein_893558..893788_NEGATIVE 297 140 91 120 47 smit:SMT_2023|5end_tryptophan_synthase,_alpha_subunit_1939315..1939545_POSITIVE 297 99 55 191 138 smit:SMT_739|5end_50S_ribosomal_protein_L7/L12_643642..643872_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 327 87 41 67 5 smit:SMT_1952|3end_hypothetical_protein_1886932..1887082_POSITIVE 322 120 71 90 46 smit:SMT_555|3end_K09015_Fe-S_cluster_assembly_protein_SufD_473613..473763_POSITIVE 306 66 39 36 13 smit:SMT_1669|3end_potassium_uptake_protein_KtrB_1658302..1658452_NEGATIVE 297 80 35 151 104 smit:SMT_1465|3end_hypothetical_protein_1446745..1446895_POSITIVE 297 99 55 118 65 smit:SMT_740|3end_50S_ribosomal_protein_L10_643715..643865_NEGATIVE 293 53 12 90 29 smit:SMT_1137|3end_K02027_multiple_sugar_transport_system_substrate-binding_protein_1078302..1078452_NEGATIVE 284 54 11 149 97 smit:SMT_1089|3end_hypothetical_protein_1024343..1024493_NEGATIVE 283 73 39 73 31 smit:SMT_1559|3end_6-phosphofructokinase_1544614..1544764_NEGATIVE 283 54 14 126 78 smit:SMT_690|3end_pyrimidine_regulatory_protein_601647..601797_NEGATIVE 281 71 36 69 23 smit:SMT_1786|3end_phenylalanyl-tRNA_synthetase_beta_chain_1763235..1763385_NEGATIVE 277 50 1 146 84 smit:SMT_1516|3end_K02029_polar_amino_acid_transport_system_permease_protein_1497489..1497639_NEGATIVE 276 53 11 151 103 smit:SMT_1024|3end_transcriptional_regulator,_MarR_family_958961..959111_NEGATIVE 275 99 55 49 8 smit:SMT_391|3end_PTS_system,_galactose-specific_IIC_component_323671..323821_POSITIVE 274 113 80 72 38 smit:SMT_1941|3end_hypothetical_protein_1877663..1877813_POSITIVE 273 144 115 33 1 smit:SMT_1954|3end_6-phospho-beta-glucosidase_1888831..1888981_POSITIVE 273 85 41 141 97 smit:SMT_1627|3end_hypothetical_protein_1616089..1616239_NEGATIVE 273 95 53 138 96 smit:SMT_903|3end_hypothetical_protein_851945..852095_NEGATIVE 267 66 24 148 96 smit:SMT_1219|3end_hypothetical_protein_1180398..1180548_POSITIVE 267 80 62 128 111 smit:SMT_997|3end_integral_membrane_protein_939243..939393_POSITIVE 265 88 41 73 27 smit:SMT_1871|3end_modification_methylase,_HemK_family_1829803..1829953_NEGATIVE