Origin IGS: ataaacctcggctgacaatataacaaattttaaataattcttccagcagtcaatagtatttttataagataccttgaaaaaaataatttgccggtgtattatttggatagatctaatgtaggttagacggacacgtgctactgcacgagctgaatttttcaggtataaatctagatttaatattaaaaaaaggtataatagaagt .........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 acttctattatacctttttttaatattaaatctagatttatacctgaaaaattcagctcgtgcagtagcacgtgtccgtctaacctacattagatctatccaaataatacaccggcaaattatttttttcaaggtatcttataaaaatactattgactgctggaagaattatttaaaatttgttatattgtcagccgaggtttat Mask Tandem Repeat Region ================================================ ataaacctcggctgacaatataacaaattttaaataattcttccagcagtcaatagtatttttataagataccttgaaaaaaataatttgccggtgtattatttggatagatctaatgtaggttagacggacacgtgctactgcacgagctgaatttttcaggtataaatctagatttaatattaaaaaaaggtataatagaagt Find is-nt database================================================ Query_seq: TDE2756:TDE2757|TDE2756:TDE2757:bacterial extracellular solute-binding protein, family 5:nucleotidyltransferase family protein:<-->:2813608..2813812 205 ataaacctcggctgacaatataacaaattttaaataattcttccagcagtcaatagtatttttataagataccttgaaaaaaataatttgccggtgtattatttggatagatctaatgtaggttagacggacacgtgctactgcacgagctgaatttttcaggtataaatctagatttaatattaaaaaaaggtataatagaagt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE2756:TDE2757|TDE2756:TDE2757:bacterial extracellular solute-binding protein, family 5:nucleotidyltransferase family protein:<-->:2813608..2813812 205 ataaacctcggctgacaatataacaaattttaaataattcttccagcagtcaatagtatttttataagataccttgaaaaaaataatttgccggtgtattatttggatagatctaatgtaggttagacggacacgtgctactgcacgagctgaatttttcaggtataaatctagatttaatattaaaaaaaggtataatagaagt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE2756:TDE2757|TDE2756:TDE2757:bacterial extracellular solute-binding protein, family 5:nucleotidyltransferase family protein:<-->:2813608..2813812 205 ataaacctcggctgacaatataacaaattttaaataattcttccagcagtcaatagtatttttataagataccttgaaaaaaataatttgccggtgtattatttggatagatctaatgtaggttagacggacacgtgctactgcacgagctgaatttttcaggtataaatctagatttaatattaaaaaaaggtataatagaagt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ataaacctcggctgacaatataacaaattttaaataattcttccagcagtcaatagtatttttataagataccttgaaaaaaataatttgccggtgtattatttggatagatctaatgtaggttagacggacacgtgctactgcacgagctgaatttttcaggtataaatctagatttaatattaaaaaaaggtataatagaagt Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: + Start: 34 End: 123 ................................. M I L P A V N S I F I R Y L E K N N L P V Y Y L D R S N V G .................................................................................. Protein_Len: 60 Strand: - Start: 1 End: 183 V E A S L I V F K L Y N K W C D I T N K Y S V K F F I I Q R H I I Q I S R I Y T L R V R A V A R A S N K L Y L D L N L M ...................... ataaacctcggctgacaatataacaaattttaaataattcttccagcagtcaatagtatttttataagataccttgaaaaaaataatttgccggtgtattatttggatagatctaatgtaggttagacggacacgtgctactgcacgagctgaatttttcaggtataaatctagatttaatattaaaaaaaggtataatagaagt 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: 86 Start: 73 End: 102 ........................................................................CTTGAAAAAAATAATTTGCCGGTGTATTAT....................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ ataaacctcggctgacaatataacaaattttaaataattcttccagcagtcaatagtatttttataagataccttgaaaaaaataatttgccggtgtattatttggatagatctaatgtaggttagacggacacgtgctactgcacgagctgaatttttcaggtataaatctagatttaatattaaaaaaaggtataatagaagt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE2756:TDE2757|TDE2756:TDE2757:bacterial extracellular solute-binding protein, family 5:nucleotidyltransferase family protein:<-->:2813608..2813812 205 ataaacctcggctgacaatataacaaattttaaataattcttccagcagtcaatagtatttttataagataccttgaaaaaaataatttgccggtgtattatttggatagatctaatgtaggttagacggacacgtgctactgcacgagctgaatttttcaggtataaatctagatttaatattaaaaaaaggtataatagaagt Intra-Species Hit: Count: 1 Min: 1 Max: 184 Len: 184 Subject: NC_002967_TDE2756_TDE2757|bacterial extracellular solute-binding protein, family 5:nucleotidyltransferase family protein|NEGATIVE:POSITIVE|[2813608,2813812]|205 HSP 1 e-value: 1.0E-87 bit: 323.0 Len: 184 Query Start:1 Query End:184 Subject Strand: POSITIVE Subject Start: 1 Subject End: 184 ataaacctcggctgacaatataacaaattttaaataattcttccagcagtcaatagtatttttataagataccttgnnnnnnntaatttgccggtgtattatttggatagatctaatgtaggttagacggacacgtgctactgcacgagctgaatttttcaggtataaatctagatttaatatt..................... ataaacctcggctgacaatataacaaattttaaataattcttccagcagtcaatagtatttttataagataccttgaaaaaaataatttgccggtgtattatttggatagatctaatgtaggttagacggacacgtgctactgcacgagctgaatttttcaggtataaatctagatttaatatt..................... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUAAACCUCGGCUGACAAUAUAACAAAUUUUAAAUAAUUCUUCCAGCAGUCAAUAGUAUUUUUAUAAGAUACCUUGAAAAAAAUAAUUUGCCGGUGUAUUAUUUGGAUAGAUCUAAUGUAGGUUAGACGGACACGUGCUACUGCACGAGCUGAAUUUUUCAGGUAUAAAUCUAGAUUUAAUAUU ..........((((.............................))))....((((.((..((((....((((((.((((((..((((((((.(((.((((.....)))).)))....))))))))..(((.(.(((((....))))).))))..)))))))))))).....))))..)).)))) (-33.85) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUAUUAAAUCUAGAUUUAUACCUGAAAAAUUCAGCUCGUGCAGUAGCACGUGUCCGUCUAACCUACAUUAGAUCUAUCCAAAUAAUACACCGGCAAAUUAUUUUUUUCAAGGUAUCUUAUAAAAAUACUAUUGACUGCUGGAAGAAUUAUUUAAAAUUUGUUAUAUUGUCAGCCGAGGUUUAU .....(((((((......((((((((((((....((.(((((....))))).))..((((((......)))))).............................)))))).))))))...............(((((.....((.(((((......))))).)).....)))))...))))))). (-30.70) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 904 140 91 231 182 NC_002967:TDE2756|5end_bacterial_extracellular_solute-binding_protein,_family_5_2813517..2813747_NEGATIVE 299 160 111 231 177 NC_002967:TDE0991|5end_ribosomal_protein_L28_1018065..1018295_NEGATIVE 275 152 111 198 159 NC_002967:TDE2640|5end_hypothetical_protein_2680034..2680264_POSITIVE 271 150 106 49 8 NC_002967:TDE0155|5end_adenylate/guanylate_cyclase_catalytic_domain_protein_180154..180384_NEGATIVE 268 160 112 87 36 NC_002967:TDE1513|5end_hypothetical_protein_1560484..1560714_POSITIVE 262 138 91 140 104 NC_002967:TDE0143|5end_thiamine_ABC_transporter,_thiamine-binding_protein_164013..164243_POSITIVE 258 169 126 57 8 NC_002967:TDE2131|5end_cobalamin_biosynthesis_protein_CbiM,_putative_2162683..2162913_NEGATIVE 258 160 113 211 159 NC_002967:TDE1604|5end_ABC_transporter,_permease_protein,_putative_1655533..1655763_NEGATIVE 256 146 107 193 157 NC_002967:TDE2632|5end_peptide_ABC_transporter,_ATP-binding_protein,_putative_2672650..2672880_POSITIVE 251 147 101 88 33 NC_002967:TDE1493|5end_chemotaxis_protein_CheX_1538590..1538820_POSITIVE 249 152 120 183 157 NC_002967:TDE2069|5end_endoribonuclease_L-PSP,_putative_2096632..2096862_POSITIVE 249 136 91 197 146 NC_002967:TDE1004|5end_flagellar_filament_core_protein_1030136..1030366_NEGATIVE 248 166 121 124 81 NC_002967:TDE2494|5end_hypothetical_protein_2518497..2518727_POSITIVE 248 153 128 231 202 NC_002967:TDE0255|5end_ABC_transporter,_ATP-binding_protein_290742..290972_NEGATIVE 243 166 126 46 5 NC_002967:TDE1987|5end_hypothetical_protein_2002312..2002542_POSITIVE 243 152 115 192 150 NC_002967:TDE1846|5end_hypothetical_protein_1875426..1875656_NEGATIVE 239 151 117 86 52 NC_002967:TDE0740|5end_hypothetical_protein_775987..776217_POSITIVE 238 149 103 227 173 NC_002967:TDE0987|5end_oligopeptide/dipeptide_ABC_transporter,_ATP-binding_protein_1014041..1014271_POSITIVE 238 168 124 62 2 NC_002967:TDE0572|5end_hypothetical_protein_603494..603724_POSITIVE 237 128 89 183 144 NC_002967:TDE1965|5end_sodium/hydrogen_exchanger_family_protein_1980151..1980381_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 278 165 123 143 91 NC_002967:TDE2066|3end_exodeoxyribonuclease_VII,_small_subunit_2092222..2092372_POSITIVE 268 160 112 74 23 NC_002967:TDE1512|3end_hypothetical_protein_1560551..1560701_POSITIVE 262 138 91 112 76 NC_002967:TDE0141|3end_hypothetical_protein_164065..164215_POSITIVE 260 162 121 124 75 NC_002967:TDE0741|3end_hypothetical_protein_776185..776335_NEGATIVE 253 139 91 74 12 NC_002967:TDE2753|3end_LysM_domain/M23/M37_peptidase_domain_protein_2809558..2809708_NEGATIVE 251 147 101 63 8 NC_002967:TDE1492|3end_chemotaxis_protein_CheW_1538645..1538795_POSITIVE 250 155 116 58 26 NC_002967:TDE0824|3end_lipoprotein,_putative_845226..845376_NEGATIVE 249 152 120 66 40 NC_002967:TDE2068|3end_antigen,_putative_2096595..2096745_POSITIVE 241 160 112 124 70 NC_002967:TDE1693|3end_hypothetical_protein_1748438..1748588_NEGATIVE 239 151 117 47 13 NC_002967:TDE0739|3end_hypothetical_protein_776028..776178_POSITIVE 237 163 121 65 32 NC_002967:TDE0837|3end_Na(+)-translocating_NADH-quinone_reductase,_B_subunit_856093..856243_NEGATIVE 236 164 121 67 24 NC_002967:TDE2317|3end_hemolysin_III_2354118..2354268_NEGATIVE 234 153 118 146 100 NC_002967:TDE2269|3end_hypothetical_protein_2304931..2305081_NEGATIVE 232 139 91 84 32 NC_002967:TDE1534|3end_hypothetical_protein_1578667..1578817_NEGATIVE 232 161 121 103 62 NC_002967:TDE1451|3end_hypothetical_protein_1497850..1498000_NEGATIVE 229 149 128 64 38 NC_002967:TDE2621|3end_hypothetical_protein_2662197..2662347_POSITIVE 223 124 87 77 29 NC_002967:TDE0940|3end_hypothetical_protein_963635..963785_POSITIVE 222 152 120 69 34 NC_002967:TDE2234|3end_iron_compound_ABC_transporter,_periplasmic_iron_compound-binding_protein,_putative_2272310..2272460_NEGATIVE 219 172 136 47 9 NC_002967:TDE2785|3end_hypothetical_protein_2838601..2838751_NEGATIVE 219 139 92 126 84 NC_002967:TDE2036|3end_ATPase,_AAA_family_2064140..2064290_NEGATIVE