Origin IGS: acttcctcccatcacatctaaaatataccacacatttttatatacatcaagagaaaaaaattgcaaaaattctattttttttaactttttacttgacaaacactatatatagtgttagaatagccgatataaggaatagaacgctaaataacggtttattccgaaagctgggaggaaaaa .........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 tttttcctcccagctttcggaataaaccgttatttagcgttctattccttatatcggctattctaacactatatatagtgtttgtcaagtaaaaagttaaaaaaaatagaatttttgcaatttttttctcttgatgtatataaaaatgtgtggtatattttagatgtgatgggaggaagt Mask Tandem Repeat Region ================================================ acttcctcccatcacatctaaaatataccacacatttttatatacatcaagagaaaaaaattgcaaaaattctattttttttaactttttacttgacaaacactatatatagtgttagaatagccgatataaggaatagaacgctaaataacggtttattccgaaagctgggaggaaaaa Find is-nt database================================================ Query_seq: TDE1854:TDE1855|TDE1854:TDE1855:nucleotidyltransferase family protein:hypothetical protein:<-->:1882806..1882985 180 acttcctcccatcacatctaaaatataccacacatttttatatacatcaagagaaaaaaattgcaaaaattctattttttttaactttttacttgacaaacactatatatagtgttagaatagccgatataaggaatagaacgctaaataacggtttattccgaaagctgggaggaaaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE1854:TDE1855|TDE1854:TDE1855:nucleotidyltransferase family protein:hypothetical protein:<-->:1882806..1882985 180 acttcctcccatcacatctaaaatataccacacatttttatatacatcaagagaaaaaaattgcaaaaattctattttttttaactttttacttgacaaacactatatatagtgttagaatagccgatataaggaatagaacgctaaataacggtttattccgaaagctgggaggaaaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE1854:TDE1855|TDE1854:TDE1855:nucleotidyltransferase family protein:hypothetical protein:<-->:1882806..1882985 180 acttcctcccatcacatctaaaatataccacacatttttatatacatcaagagaaaaaaattgcaaaaattctattttttttaactttttacttgacaaacactatatatagtgttagaatagccgatataaggaatagaacgctaaataacggtttattccgaaagctgggaggaaaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 acttcctcccatcacatctaaaatataccacacatttttatatacatcaagagaaaaaaattgcaaaaattctattttttttaactttttacttgacaaacactatatatagtgttagaatagccgatataaggaatagaacgctaaataacggtttattccgaaagctgggaggaaaaa Predict ORF larger than 30AA ================================================ Protein_Len: 33 Strand: + Start: 11 End: 109 .......... M T S K I Y H T F L Y T S R E K N C K N S I F F N F L L D K H Y I ....................................................................... Protein_Len: 46 Strand: + Start: 42 End: 179 ......................................... M H Q E K K I A K I L F F L T F Y L T N T I Y S V R I A D I R N R T L N N G L F R K L G G K . Protein_Len: 33 Strand: - Start: 1 End: 99 S G G M V D L I Y W V N K Y V D L S F F Q L F E I K K L K K S S M ................................................................................. acttcctcccatcacatctaaaatataccacacatttttatatacatcaagagaaaaaaattgcaaaaattctattttttttaactttttacttgacaaacactatatatagtgttagaatagccgatataaggaatagaacgctaaataacggtttattccgaaagctgggaggaaaaa 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: 91 Start: 92 End: 121 ...........................................................................................CTTGACAAACACTATATATAGTGTTAGAAT........................................................... PromScan Matrix: RpoD-17 Strand: - Score: 85 Start: 22 End: 51 .....................CTTGATGTATATAAAAATGTGTGGTATATT................................................................................................................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ acttcctcccatcacatctaaaatataccacacatttttatatacatcaagagaaaaaaattgcaaaaattctattttttttaactttttacttgacaaacactatatatagtgttagaatagccgatataaggaatagaacgctaaataacggtttattccgaaagctgggaggaaaaa Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE1854:TDE1855|TDE1854:TDE1855:nucleotidyltransferase family protein:hypothetical protein:<-->:1882806..1882985 180 acttcctcccatcacatctaaaatataccacacatttttatatacatcaagagaaaaaaattgcaaaaattctattttttttaactttttacttgacaaacactatatatagtgttagaatagccgatataaggaatagaacgctaaataacggtttattccgaaagctgggaggaaaaa Intra-Species Hit: Count: 1 Min: 1 Max: 180 Len: 180 Subject: NC_002967_TDE1854_TDE1855|nucleotidyltransferase family protein:hypothetical protein|NEGATIVE:POSITIVE|[1882806,1882985]|180 HSP 1 e-value: 6.0E-71 bit: 268.0 Len: 180 Query Start:1 Query End:180 Subject Strand: POSITIVE Subject Start: 1 Subject End: 180 acttcctcccatcacatctaaaatataccacacatttttatatacatcaagagnnnnnnnttgcaaaaattctannnnnnnnaactttttacttgacaaacactatatatagtgttagaatagccgatataaggaatagaacgctaaataacggtttattccgaaagctgggaggaaaaa acttcctcccatcacatctaaaatataccacacatttttatatacatcaagagaaaaaaattgcaaaaattctattttttttaactttttacttgacaaacactatatatagtgttagaatagccgatataaggaatagaacgctaaataacggtttattccgaaagctgggaggaaaaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACUUCCUCCCAUCACAUCUAAAAUAUACCACACAUUUUUAUAUACAUCAAGAGAAAAAAAUUGCAAAAAUUCUAUUUUUUUUAACUUUUUACUUGACAAACACUAUAUAUAGUGUUAGAAUAGCCGAUAUAAGGAAUAGAACGCUAAAUAACGGUUUAUUCCGAAAGCUGGGAGGAAAAA ..(((((((((.(........................((((((...(((((.(((((...(((.(((((......))))).))).))))).)))))..(((((((....)))))))..........))))))((((((((.((........)).))))))))....).)))))))))... (-39.30) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUUUCCUCCCAGCUUUCGGAAUAAACCGUUAUUUAGCGUUCUAUUCCUUAUAUCGGCUAUUCUAACACUAUAUAUAGUGUUUGUCAAGUAAAAAGUUAAAAAAAAUAGAAUUUUUGCAAUUUUUUUCUCUUGAUGUAUAUAAAAAUGUGUGGUAUAUUUUAGAUGUGAUGGGAGGAAGU ..((((((((((......((((((...((((....))))...)))))).((((((.(((((.(.(((((((....))))))).((((((.((((((((..(((((......)))))..))))))))...))))))............).)))))........)))))).)))))))))). (-46.00) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 782 140 91 231 182 NC_002967:TDE1854|5end_nucleotidyltransferase_family_protein_1882715..1882945_NEGATIVE 305 130 94 199 167 NC_002967:TDE1330|5end_conserved_hypothetical_protein_TIGR00244_1365379..1365609_POSITIVE 265 155 111 71 27 NC_002967:TDE0866|5end_hypothetical_protein_887614..887844_POSITIVE 261 146 111 57 21 NC_002967:TDE0364|5end_ABC_transporter,_ATP-binding_protein_411605..411835_NEGATIVE 259 179 148 177 142 NC_002967:TDE1424|5end_hypothetical_protein_1467135..1467365_POSITIVE 258 156 120 177 131 NC_002967:TDE1390|5end_hypothetical_protein_1429692..1429922_POSITIVE 256 170 124 52 4 NC_002967:TDE2335|5end_ATP-dependent_DNA_helicase,_UvrD/Rep_family_2369641..2369871_POSITIVE 254 175 133 72 29 NC_002967:TDE0072|5end_methyl-accepting_chemotaxis_protein_80921..81151_POSITIVE 248 175 132 166 121 NC_002967:TDE1031|5end_hypothetical_protein_1060010..1060240_POSITIVE 243 174 131 223 172 NC_002967:TDE0950|5end_hypothetical_protein_974312..974542_NEGATIVE 240 174 138 72 32 NC_002967:TDE1454|5end_sugar_transporter_1501438..1501668_POSITIVE 238 159 122 230 188 NC_002967:TDE0566|5end_hypothetical_protein_597185..597415_POSITIVE 238 159 122 76 34 NC_002967:TDE0565|5end_hypothetical_protein_597031..597261_POSITIVE 237 169 122 180 123 NC_002967:TDE1552|5end_hypothetical_protein_1595759..1595989_POSITIVE 235 170 123 123 71 NC_002967:TDE2628|5end_hypothetical_protein_2669068..2669298_POSITIVE 232 154 123 199 173 NC_002967:TDE0821|5end_hypothetical_protein_844378..844608_POSITIVE 226 170 132 84 32 NC_002967:TDE0759|5end_hypothetical_protein_799499..799729_NEGATIVE 225 174 142 203 163 NC_002967:TDE0250|5end_sodium-dependent_transporter,_putative_284635..284865_NEGATIVE 220 170 123 201 151 NC_002967:TDE1907|5end_holo-(acyl-carrier-protein)_synthase_1925097..1925327_NEGATIVE 218 175 133 171 138 NC_002967:TDE2347|5end_30S_ribosomal_protein_S2_2384378..2384608_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 305 130 94 86 54 NC_002967:TDE1329|3end_ATPase,_AAA_family_1365346..1365496_POSITIVE 250 163 125 139 106 NC_002967:TDE2409|3end_hypothetical_protein_2435485..2435635_NEGATIVE 248 175 132 118 73 NC_002967:TDE1030|3end_hypothetical_protein_1060042..1060192_POSITIVE 244 170 123 65 10 NC_002967:TDE1934|3end_hypothetical_protein_1952804..1952954_POSITIVE 240 174 138 70 30 NC_002967:TDE1453|3end_alpha-galactosidase_1501516..1501666_POSITIVE 233 145 116 39 16 NC_002967:TDE0166|3end_hypothetical_protein_195050..195200_NEGATIVE 231 171 131 146 114 NC_002967:TDE1103|3end_hypothetical_protein_1136670..1136820_POSITIVE 231 173 149 55 21 NC_002967:TDE0978|3end_hypothetical_protein_1002424..1002574_POSITIVE 228 179 152 80 52 NC_002967:TDE0493|3end_hypothetical_protein_548581..548731_NEGATIVE 227 177 139 125 80 NC_002967:TDE2219|3end_hypothetical_protein_2258961..2259111_NEGATIVE 227 176 132 146 95 NC_002967:TDE1743|3end_chromate_transport_protein_1797940..1798090_NEGATIVE 225 174 142 121 81 NC_002967:TDE0251|3end_tryptophanase_284717..284867_NEGATIVE 224 174 131 143 106 NC_002967:TDE0038|3end_3-oxoacyl-(acyl-carrier-protein)_synthase_II_43036..43186_NEGATIVE 221 175 131 112 74 NC_002967:TDE0604|3end_hypothetical_protein_641831..641981_NEGATIVE 217 176 153 31 4 NC_002967:TDE1451|3end_hypothetical_protein_1497850..1498000_NEGATIVE 213 175 131 116 81 NC_002967:TDE1105|3end_ribosome-binding_factor_A_1137801..1137951_NEGATIVE 212 174 137 133 92 NC_002967:TDE1612|3end_phosphoribosyl_transferase_domain_protein_1661690..1661840_POSITIVE 211 178 131 76 32 NC_002967:TDE2242|3end_antigen,_putative_2279569..2279719_NEGATIVE 209 175 132 53 20 NC_002967:TDE0360|3end_ABC_transporter,_ATP-binding/permease_protein_404102..404252_NEGATIVE 208 167 122 87 55 NC_002967:TDE0745|3end_glycine_reductase_complex_selenoprotein_GrdA_780840..780990_POSITIVE