Origin IGS: tagatacctccaagaaacgcaaaaagcctactggattttcagtaggtttcaatctatatttttcacatatttttattaggttatatatatatatatatatatatatatatatgcatttgcgtagtctgactcattttgaactcctttagaattaaattttcagagatgctataaacaattctaataactctcagcctaaaactattataccatgatttctattttttcaaaaaaacgaaccagattaactgattcgtttcgtgactgctaatctc .........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 gagattagcagtcacgaaacgaatcagttaatctggttcgtttttttgaaaaaatagaaatcatggtataatagttttaggctgagagttattagaattgtttatagcatctctgaaaatttaattctaaaggagttcaaaatgagtcagactacgcaaatgcatatatatatatatatatatatatatatataacctaataaaaatatgtgaaaaatatagattgaaacctactgaaaatccagtaggctttttgcgtttcttggaggtatcta Mask Tandem Repeat Region ================================================ tagatacctccaagaaacgcaaaaagcctactggattttcagtaggtttcaatctatatttttcacatatttttattaggtnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnngcatttgcgtagtctgactcattttgaactcctttagaattaaattttcagagatgctataaacaattctaataactctcagcctaaaactattataccatgatttctattttttcaaaaaaacgaaccagattaactgattcgtttcgtgactgctaatctc Find is-nt database================================================ Query_seq: SMT_768:SMT_769|SMT_768:SMT_769:hypothetical protein:spermidine/putrescine-binding periplasmic protein:<-<-:679334..679608 275 tagatacctccaagaaacgcaaaaagcctactggattttcagtaggtttcaatctatatttttcacatatttttattaggttatatatatatatatatatatatatatatatgcatttgcgtagtctgactcattttgaactcctttagaattaaattttcagagatgctataaacaattctaataactctcagcctaaaactattataccatgatttctattttttcaaaaaaacgaaccagattaactgattcgtttcgtgactgctaatctc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_768:SMT_769|SMT_768:SMT_769:hypothetical protein:spermidine/putrescine-binding periplasmic protein:<-<-:679334..679608 275 tagatacctccaagaaacgcaaaaagcctactggattttcagtaggtttcaatctatatttttcacatatttttattaggttatatatatatatatatatatatatatatatgcatttgcgtagtctgactcattttgaactcctttagaattaaattttcagagatgctataaacaattctaataactctcagcctaaaactattataccatgatttctattttttcaaaaaaacgaaccagattaactgattcgtttcgtgactgctaatctc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_768:SMT_769|SMT_768:SMT_769:hypothetical protein:spermidine/putrescine-binding periplasmic protein:<-<-:679334..679608 275 tagatacctccaagaaacgcaaaaagcctactggattttcagtaggtttcaatctatatttttcacatatttttattaggttatatatatatatatatatatatatatatatgcatttgcgtagtctgactcattttgaactcctttagaattaaattttcagagatgctataaacaattctaataactctcagcctaaaactattataccatgatttctattttttcaaaaaaacgaaccagattaactgattcgtttcgtgactgctaatctc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tagatacctccaagaaacgcaaaaagcctactggattttcagtaggtttcaatctatatttttcacatatttttattaggttatatatatatatatatatatatatatatatgcatttgcgtagtctgactcattttgaactcctttagaattaaattttcagagatgctataaacaattctaataactctcagcctaaaactattataccatgatttctattttttcaaaaaaacgaaccagattaactgattcgtttcgtgactgctaatctc Predict ORF larger than 30AA ================================================ Protein_Len: 37 Strand: - Start: 84 End: 194 ................................................................................... I Y I Y I Y I Y I H M Q T T Q S M K F E K L I L N E S I S Y V I R I V R M ................................................................................. Protein_Len: 37 Strand: - Start: 2 End: 112 . S V E L F R L F G V P N E T P K L R Y K E C I K I L N Y I Y I Y I Y I Y M ................................................................................................................................................................... tagatacctccaagaaacgcaaaaagcctactggattttcagtaggtttcaatctatatttttcacatatttttattaggttatatatatatatatatatatatatatatatgcatttgcgtagtctgactcattttgaactcctttagaattaaattttcagagatgctataaacaattctaataactctcagcctaaaactattataccatgatttctattttttcaaaaaaacgaaccagattaactgattcgtttcgtgactgctaatctc 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: 84 Start: 204 End: 233 ...........................................................................................................................................................................................................TTTTTGAAAAAATAGAAATCATGGTATAAT.......................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tagatacctccaagaaacgcaaaaagcctactggattttcagtaggtttcaatctatatttttcacatatttttattaggttatatatatatatatatatatatatatatatgcatttgcgtagtctgactcattttgaactcctttagaattaaattttcagagatgctataaacaattctaataactctcagcctaaaactattataccatgatttctattttttcaaaaaaacgaaccagattaactgattcgtttcgtgactgctaatctc Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 69 HP_score: -4.4 Tail_Score: -4.86939 Start: 26 End: 47 Full_Region: aaaatatagattgaa acctactg aaaatc cagtaggc tttttgcgtttcttg .........................acctactgaaaatccagtaggc.................................................................................................................................................................................................................................... TransTerm Strand: - Conf: 74 HP_score: -7.9 Tail_Score: -3.50537 Start: 27 End: 46 Full_Region: aaatatagattgaaa cctactg aaaatc cagtagg ctttttgcgtttctt ..........................cctactgaaaatccagtagg..................................................................................................................................................................................................................................... TransTerm Strand: + Conf: 75 HP_score: -9.7 Tail_Score: -2.66748 Start: 82 End: 111 Full_Region: ATATTTTTATTAGGT TATATATATATAT ATAT ATATATATATATA TGCATTTGCGTAGTC .................................................................................TATATATATATATATATATATATATATATA.................................................................................................................................................................... TransTerm Strand: + Conf: 60 HP_score: -5.4 Tail_Score: -3.77196 Start: 236 End: 256 Full_Region: ATTTTTTCAAAAAAA CGAACCAG ATTAA CTGATTCG TTTCGTGACTGCTAA ...........................................................................................................................................................................................................................................CGAACCAGATTAACTGATTCG................... Find igs database================================================ Query_seq: SMT_768:SMT_769|SMT_768:SMT_769:hypothetical protein:spermidine/putrescine-binding periplasmic protein:<-<-:679334..679608 275 tagatacctccaagaaacgcaaaaagcctactggattttcagtaggtttcaatctatatttttcacatatttttattaggttatatatatatatatatatatatatatatatgcatttgcgtagtctgactcattttgaactcctttagaattaaattttcagagatgctataaacaattctaataactctcagcctaaaactattataccatgatttctattttttcaaaaaaacgaaccagattaactgattcgtttcgtgactgctaatctc Intra-Species Hit: Count: 1 Min: 1 Max: 275 Len: 275 Subject: smit_SMT_768_SMT_769|hypothetical protein:spermidine/putrescine-binding periplasmic protein|NEGATIVE:NEGATIVE|[679334,679608]|275 HSP 1 e-value: 6.0E-75 bit: 281.0 Len: 163 Query Start:113 Query End:275 Subject Strand: POSITIVE Subject Start: 113 Subject End: 275 ................................................................................................................gcatttgcgtagtctgactcattttgaactcctttagaattaaattttcagagatgctataaacaattctaataactctcagcctaaaactattataccatgatttctattttttcnnnnnnncgaaccagattaactgattcgtttcgtgactgctaatctc ................................................................................................................gcatttgcgtagtctgactcattttgaactcctttagaattaaattttcagagatgctataaacaattctaataactctcagcctaaaactattataccatgatttctattttttcaaaaaaacgaaccagattaactgattcgtttcgtgactgctaatctc HSP 2 e-value: 2.0E-38 bit: 161.0 Len: 81 Query Start:1 Query End:81 Subject Strand: POSITIVE Subject Start: 1 Subject End: 81 tagatacctccaagaaacgcaaaaagcctactggattttcagtaggtttcaatctatatttttcacatatttttattaggt.................................................................................................................................................................................................. tagatacctccaagaaacgcaaaaagcctactggattttcagtaggtttcaatctatatttttcacatatttttattaggt.................................................................................................................................................................................................. Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAGAUACCUCCAAGAAACGCAAAAAGCCUACUGGAUUUUCAGUAGGUUUCAAUCUAUAUUUUUCACAUAUUUUUAUUAGGUUAUAUAUAUAUAUAUAUAUAUAUAUAUAUAUGCAUUUGCGUAGUCUGACUCAUUUUGAACUCCUUUAGAAUUAAAUUUUCAGAGAUGCUAUAAACAAUUCUAAUAACUCUCAGCCUAAAACUAUUAUACCAUGAUUUCUAUUUUUUCAAAAAAACGAACCAGAUUAACUGAUUCGUUUCGUGACUGCUAAUCUC ............(((...(((..(((((((((((....))))))))))).............((((.........(((((((.(((((((((((((....))))))))))))).....((((..(((((...((((((((....)))))))).......))))).)))).......................))))))).................................(((((((.(((.....))).))))))).)))).)))...))). (-54.60) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAGAUUAGCAGUCACGAAACGAAUCAGUUAAUCUGGUUCGUUUUUUUGAAAAAAUAGAAAUCAUGGUAUAAUAGUUUUAGGCUGAGAGUUAUUAGAAUUGUUUAUAGCAUCUCUGAAAAUUUAAUUCUAAAGGAGUUCAAAAUGAGUCAGACUACGCAAAUGCAUAUAUAUAUAUAUAUAUAUAUAUAUAUAUAACCUAAUAAAAAUAUGUGAAAAAUAUAGAUUGAAACCUACUGAAAAUCCAGUAGGCUUUUUGCGUUUCUUGGAGGUAUCUA ...........(((.((((((((((((.....))))))))))))..))).....((((.(((.((.((((((((((((((..(....)...))))))))).))))).))..(((((..(((((((((.....)))))..))))...)))))..(((((((....(((((((((((((....)))))))))))))............(((((.....)))))........(((((((......)))))))...)))))))........))).)))) (-63.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 869 50 1 141 92 smit:SMT_768|5end_hypothetical_protein_679243..679473_NEGATIVE 292 154 114 68 29 smit:SMT_841|5end_dihydrodipicolinate_reductase_788025..788255_NEGATIVE 265 61 26 68 35 smit:SMT_567|5end_conserved_hypothetical_protein_484845..485075_POSITIVE 251 266 221 226 177 smit:SMT_547|5end_branched-chain_amino_acid_aminotransferase_463947..464177_POSITIVE 242 56 14 95 48 smit:SMT_157|5end_hypothetical_protein_103525..103755_POSITIVE 240 50 8 154 115 smit:SMT_226|5end_putative_L-glutamine-D-fructose-6-phosphate_amidotransferase_163630..163860_POSITIVE 236 51 17 158 120 smit:SMT_331|5end_endo-beta-N-acetylglucosaminidase_266416..266646_POSITIVE 235 47 7 59 6 smit:SMT_2063|5end_hypothetical_protein_1971792..1972022_NEGATIVE 235 47 7 98 45 smit:SMT_1996|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1921078..1921308_NEGATIVE 234 265 236 72 44 smit:SMT_1398|5end_dihydroorotase_1373204..1373434_POSITIVE 233 48 7 231 198 smit:SMT_1205|5end_response_regulator_1165700..1165930_NEGATIVE 232 150 112 169 137 smit:SMT_426|5end_hypothetical_protein_368344..368574_POSITIVE 231 168 121 124 73 smit:SMT_1714|5end_hypothetical_membrane_spanning_protein_1701356..1701586_POSITIVE 231 150 111 58 8 smit:SMT_692|5end_hypothetical_protein_603550..603780_NEGATIVE 230 145 117 95 70 smit:SMT_623|5end_50S_ribosomal_protein_L21_529412..529642_POSITIVE 229 160 112 209 159 smit:SMT_2165|5end_K06147_ATP-binding_cassette,_subfamily_B,_bacterial_2038681..2038911_POSITIVE 229 169 126 201 158 smit:SMT_1371|5end_hypothetical_protein_1350794..1351024_NEGATIVE 229 47 7 140 96 smit:SMT_1247|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1207409..1207639_POSITIVE 229 169 124 133 84 smit:SMT_945|5end_cytidylate_kinase_895908..896138_NEGATIVE 228 147 116 104 75 smit:SMT_2065|5end_transcriptional_regulator,_MarR_family_1972665..1972895_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 265 61 26 46 13 smit:SMT_566|3end_K07282_poly-gamma-glutamate_synthesis_protein_(capsule_biosynthesis_protein)_484903..485053_POSITIVE 263 269 221 100 42 smit:SMT_546|3end_DNA_topoisomerase_IV_subunit_A_463892..464042_POSITIVE 250 49 7 78 21 smit:SMT_605|3end_DNA-binding_protein_HU_519257..519407_POSITIVE 238 220 178 51 3 smit:SMT_156|3end_hypothetical_protein_103518..103668_POSITIVE 235 270 230 54 17 smit:SMT_1128|3end_surface_antigen_1061935..1062085_NEGATIVE 234 265 236 59 31 smit:SMT_1397|3end_mutator_MutT_protein_1373271..1373421_POSITIVE 231 168 121 112 61 smit:SMT_1713|3end_K03284_metal_ion_transporter,_MIT_family_1701424..1701574_POSITIVE 230 145 117 44 19 smit:SMT_622|3end_methionine_aminopeptidase_529441..529591_POSITIVE 229 169 124 123 74 smit:SMT_946|3end_hypothetical_protein_895918..896068_NEGATIVE 223 203 161 147 108 smit:SMT_2125|3end_3-phosphoshikimate_1-carboxyvinyltransferase_2009098..2009248_POSITIVE 222 49 8 92 53 smit:SMT_226|3end_putative_L-glutamine-D-fructose-6-phosphate_amidotransferase_164000..164150_POSITIVE 222 49 8 92 53 smit:SMT_223|3end_D-fructose-6-phosphate_amidotransferase_158431..158581_POSITIVE 221 49 2 77 22 smit:SMT_1491|3end_capsular_polysaccharide_biosynthesis_protein,_putative_1471967..1472117_POSITIVE 218 59 12 131 72 smit:SMT_363|3end_K02519_translation_initiation_factor_IF-2_300751..300901_POSITIVE 215 75 32 122 81 smit:SMT_737|3end_hypothetical_protein_642270..642420_NEGATIVE 215 48 7 134 95 smit:SMT_603|3end_hypothetical_protein_518532..518682_POSITIVE 214 148 112 93 48 smit:SMT_1635|3end_putative_N-acetyldiaminopimelate_deacetylase_1622636..1622786_POSITIVE 213 270 235 45 1 smit:SMT_1383|3end_ribonucleoside-diphosphate_reductase_alpha_chain_1360795..1360945_NEGATIVE 210 266 235 147 117 smit:SMT_1324|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1294036..1294186_POSITIVE 210 259 218 89 35 smit:SMT_992|3end_hypothetical_protein_934529..934679_NEGATIVE