Origin IGS: atattctcccttgttctcatattatccttcaaaaatatctttgattttttctccagattcatatacaataaatacaatgcttattataccataaatccgctttcaacgataaagaaaaggtaagaaaa .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ttttcttaccttttctttatcgttgaaagcggatttatggtataataagcattgtatttattgtatatgaatctggagaaaaaatcaaagatatttttgaaggataatatgagaacaagggagaatat Mask Tandem Repeat Region ================================================ atattctcccttgttctcatattatccttcaaaaatatctttgattttttctccagattcatatacaataaatacaatgcttattataccataaatccgctttcaacgataaagaaaaggtaagaaaa Find is-nt database================================================ Query_seq: SMT_666:SMT_667|SMT_666:SMT_667:GTP pyrophosphokinase-like protein:hypothetical protein:<-->:577491..577618 128 atattctcccttgttctcatattatccttcaaaaatatctttgattttttctccagattcatatacaataaatacaatgcttattataccataaatccgctttcaacgataaagaaaaggtaagaaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_666:SMT_667|SMT_666:SMT_667:GTP pyrophosphokinase-like protein:hypothetical protein:<-->:577491..577618 128 atattctcccttgttctcatattatccttcaaaaatatctttgattttttctccagattcatatacaataaatacaatgcttattataccataaatccgctttcaacgataaagaaaaggtaagaaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_666:SMT_667|SMT_666:SMT_667:GTP pyrophosphokinase-like protein:hypothetical protein:<-->:577491..577618 128 atattctcccttgttctcatattatccttcaaaaatatctttgattttttctccagattcatatacaataaatacaatgcttattataccataaatccgctttcaacgataaagaaaaggtaagaaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 atattctcccttgttctcatattatccttcaaaaatatctttgattttttctccagattcatatacaataaatacaatgcttattataccataaatccgctttcaacgataaagaaaaggtaagaaaa Predict ORF larger than 30AA ================================================ Protein_Len: 40 Strand: + Start: 1 End: 120 M F S L V L I L S F K N I F D F F S R F I Y N K Y N A Y Y T I N P L S T I K K R ........ atattctcccttgttctcatattatccttcaaaaatatctttgattttttctccagattcatatacaataaatacaatgcttattataccataaatccgctttcaacgataaagaaaaggtaagaaaa 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: 40 End: 69 .......................................TTTGATTTTTTCTCCAGATTCATATACAAT........................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ atattctcccttgttctcatattatccttcaaaaatatctttgattttttctccagattcatatacaataaatacaatgcttattataccataaatccgctttcaacgataaagaaaaggtaagaaaa Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_666:SMT_667|SMT_666:SMT_667:GTP pyrophosphokinase-like protein:hypothetical protein:<-->:577491..577618 128 atattctcccttgttctcatattatccttcaaaaatatctttgattttttctccagattcatatacaataaatacaatgcttattataccataaatccgctttcaacgataaagaaaaggtaagaaaa Intra-Species Hit: Count: 1 Min: 1 Max: 128 Len: 128 Subject: smit_SMT_666_SMT_667|GTP pyrophosphokinase-like protein:hypothetical protein|NEGATIVE:POSITIVE|[577491,577618]|128 HSP 1 e-value: 6.0E-67 bit: 254.0 Len: 128 Query Start:1 Query End:128 Subject Strand: POSITIVE Subject Start: 1 Subject End: 128 atattctcccttgttctcatattatccttcaaaaatatctttgattttttctccagattcatatacaataaatacaatgcttattataccataaatccgctttcaacgataaagaaaaggtaagaaaa atattctcccttgttctcatattatccttcaaaaatatctttgattttttctccagattcatatacaataaatacaatgcttattataccataaatccgctttcaacgataaagaaaaggtaagaaaa Inter-species Hit: Count: 3 Min: 1 Max: 128 Len: 128 Subject: NC_008533_SPD_0981_SPD_0982|adenylate cyclase, putative:pyrophosphokinase family protein|NEGATIVE:POSITIVE|[994457,994583]|127 HSP 1 e-value: 9.0E-60 bit: 230.0 Len: 128 Query Start:1 Query End:128 Subject Strand: NEGATIVE Subject Start: 1 Subject End: 127 atattctcccttgttctcatattatccttcaaaaatatctttgattttttctccagattcatatacaataaatacaatgcttattataccataaatccgctttcaacgataaagaaaaggtaagaaaa atattctcccttgttctcatattatccgtcaaaaatatctttgattttttctccagattcatatacaataaatacaatgcttattataccataaatccgctttcaacgataaa-aaaaggtaagaaaa Subject: NC_003098_spr1003_spr1004|hypothetical protein:Similar to GTP pyrophosphokinase|NEGATIVE:POSITIVE|[986926,987052]|127 HSP 1 e-value: 9.0E-60 bit: 230.0 Len: 128 Query Start:1 Query End:128 Subject Strand: NEGATIVE Subject Start: 1 Subject End: 127 atattctcccttgttctcatattatccttcaaaaatatctttgattttttctccagattcatatacaataaatacaatgcttattataccataaatccgctttcaacgataaagaaaaggtaagaaaa atattctcccttgttctcatattatccgtcaaaaatatctttgattttttctccagattcatatacaataaatacaatgcttattataccataaatccgctttcaacgataaa-aaaaggtaagaaaa Subject: NC_003028_SP_1096_SP_1097|hypothetical protein:hypothetical protein|NEGATIVE:POSITIVE|[1030349,1030475]|127 HSP 1 e-value: 9.0E-60 bit: 230.0 Len: 128 Query Start:1 Query End:128 Subject Strand: NEGATIVE Subject Start: 1 Subject End: 127 atattctcccttgttctcatattatccttcaaaaatatctttgattttttctccagattcatatacaataaatacaatgcttattataccataaatccgctttcaacgataaagaaaaggtaagaaaa atattctcccttgttctcatattatccgtcaaaaatatctttgattttttctccagattcatatacaataaatacaatgcttattataccataaatccgctttcaacgataaa-aaaaggtaagaaaa Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUAUUCUCCCUUGUUCUCAUAUUAUCCUUCAAAAAUAUCUUUGAUUUUUUCUCCAGAUUCAUAUACAAUAAAUACAAUGCUUAUUAUACCAUAAAUCCGCUUUCAACGAUAAAGAAAAGGUAAGAAAA ...((((..(((.((((....(((((..(((((......)))))..................................((..(((........)))..)).......))))))))).)))..)))).. (-11.00) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUUCUUACCUUUUCUUUAUCGUUGAAAGCGGAUUUAUGGUAUAAUAAGCAUUGUAUUUAUUGUAUAUGAAUCUGGAGAAAAAAUCAAAGAUAUUUUUGAAGGAUAAUAUGAGAACAAGGGAGAAUAU ..(((((.(((((((((((((........((((((((((.(((((((((.......))))))))))))))))))).........((((((....))))))..))))....))))).)))))))))... (-28.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 769 100 51 191 142 smit:SMT_666|5end_GTP_pyrophosphokinase-like_protein_577400..577630_NEGATIVE 236 90 42 133 91 smit:SMT_1796|5end_dihydroorotate_dehydrogenase_A_1770816..1771046_NEGATIVE 219 111 82 160 128 smit:SMT_647|5end_DNA_gyrase,_A_subunit_554170..554400_NEGATIVE 217 120 75 158 109 smit:SMT_596|5end_K03976_putative_transcription_regulator_513075..513305_NEGATIVE 216 46 4 145 99 smit:SMT_1170|5end_acetyltransferase,_CysE/LacA/LpxA/NodL_family_1118126..1118356_NEGATIVE 213 35 4 140 99 smit:SMT_1560|5end_DNA_polymerase_III_alpha_subunit_1548612..1548842_NEGATIVE 213 45 5 135 98 smit:SMT_1049|5end_hypothetical_protein_988438..988668_POSITIVE 213 53 22 113 81 smit:SMT_288|5end_hypothetical_protein_231184..231414_POSITIVE 206 27 1 123 90 smit:SMT_745|5end_glycosyl_transferase,_group_1_family_protein_650387..650617_NEGATIVE 204 93 51 61 12 smit:SMT_1880|5end_hypothetical_protein_1836854..1837084_POSITIVE 199 48 10 123 79 smit:SMT_99|5end_tRNA(Ile)-lysidine_synthetase_30189..30419_POSITIVE 198 47 9 51 13 smit:SMT_2161|5end_DNA_mismatch_repair_protein_2034946..2035176_POSITIVE 197 60 14 187 142 smit:SMT_1734|5end_serine/threonine_protein_phosphatase_1718558..1718788_POSITIVE 197 59 26 105 76 smit:SMT_337|5end_hypothetical_protein_275539..275769_POSITIVE 196 56 11 50 5 smit:SMT_1946|5end_sucrose-6-phosphate_hydrolase_1880802..1881032_POSITIVE 196 54 13 225 182 smit:SMT_1680|5end_hypothetical_protein_1663494..1663724_POSITIVE 196 56 11 50 5 smit:SMT_914|5end_sucrose-6-phosphate_hydrolase_866139..866369_POSITIVE 194 27 6 225 204 smit:SMT_1866|5end_extramembranal_protein_1827290..1827520_POSITIVE 194 27 6 225 204 smit:SMT_1313|5end_extramembranal_protein_1277274..1277504_POSITIVE 194 58 13 109 60 smit:SMT_749|5end_shikimate_kinase_653971..654201_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 216 46 4 49 3 smit:SMT_1171|3end_hypothetical_protein_1118222..1118372_NEGATIVE 213 45 5 138 101 smit:SMT_1048|3end_K06518_holin-like_protein_988521..988671_POSITIVE 213 53 22 123 91 smit:SMT_287|3end_UDP-galactopyranose_mutase_231274..231424_POSITIVE 212 40 6 36 6 smit:SMT_1864|3end_integral_membrane_protein_1827172..1827322_POSITIVE 208 117 81 47 13 smit:SMT_777|3end_hypothetical_protein_686618..686768_NEGATIVE 206 27 1 133 100 smit:SMT_746|3end_LPS_biosynthesis_protein_650377..650527_NEGATIVE 199 48 10 126 82 smit:SMT_98|3end_hypothetical_protein_30272..30422_POSITIVE 198 49 3 145 98 smit:SMT_1442|3end_hypothetical_protein_1425762..1425912_NEGATIVE 197 59 26 108 79 smit:SMT_336|3end_hypothetical_protein_275622..275772_POSITIVE 194 58 13 116 67 smit:SMT_750|3end_3-phosphoshikimate_1-carboxyvinyltransferase_653964..654114_NEGATIVE 189 54 13 97 50 smit:SMT_1381|3end_gamma-glutamyl_phosphate_reductase_1358468..1358618_NEGATIVE 187 108 77 81 45 smit:SMT_565|3end_polypeptide_deformylase_482762..482912_NEGATIVE 186 58 13 103 62 smit:SMT_603|3end_hypothetical_protein_518532..518682_POSITIVE 185 28 5 137 110 smit:SMT_1876|3end_transcriptional_regulator,_MarR_family_1834135..1834285_POSITIVE 181 34 2 81 47 smit:SMT_1206|3end_similar_to_sensor_histidine_kinase_(AgrC_from_Staphylococcus)_1165697..1165847_NEGATIVE 181 60 25 96 53 smit:SMT_367|3end_hypothetical_protein_303732..303882_POSITIVE 179 46 1 107 67 smit:SMT_1513|3end_hypothetical_protein_1494761..1494911_NEGATIVE 176 50 10 131 85 smit:SMT_449|3end_hypothetical_protein_388219..388369_POSITIVE 174 44 4 70 33 smit:SMT_1930|3end_peptide_chain_release_factor_1_1869785..1869935_NEGATIVE 174 99 51 115 59 smit:SMT_1633|3end_formate--tetrahydrofolate_ligase_1620990..1621140_POSITIVE