Origin IGS: aaagaataaataattttgggattaagggaaccgctgcatttgcagaggaaagtccggactccttcggaaacgatgccggctaacggccggggaacggaaattaaagtttccgtttacagacagtgcaacagaaagtaaaccgccgcattttgcggtaagggtgaaagggcggggtaagagcccaccgcgttttcggtaacggaaacggcaatgtaaacctcatcgggagcaaggttaagcagtaaagaatctccgattcttaatttacgggttaaccgcgataaaaacttgctgtaaagcgggtttaagaaagatggttccgtctgttttacagaaacagaatccggcttattaatccctttttttaaggtattataaaa .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9 ttttataataccttaaaaaaagggattaataagccggattctgtttctgtaaaacagacggaaccatctttcttaaacccgctttacagcaagtttttatcgcggttaacccgtaaattaagaatcggagattctttactgcttaaccttgctcccgatgaggtttacattgccgtttccgttaccgaaaacgcggtgggctcttaccccgccctttcacccttaccgcaaaatgcggcggtttactttctgttgcactgtctgtaaacggaaactttaatttccgttccccggccgttagccggcatcgtttccgaaggagtccggactttcctctgcaaatgcagcggttcccttaatcccaaaattatttattcttt Mask Tandem Repeat Region ================================================ aaagaataaataattttgggattaagggaaccgctgcatttgcagaggaaagtccggactccttcggaaacgatgccggctaacggccggggaacggaaattaaagtttccgtttacagacagtgcaacagaaagtaaaccgccgcattttgcggtaagggtgaaagggcggggtaagagcccaccgcgttttcggtaacggaaacggcaatgtaaacctcatcgggagcaaggttaagcagtaaagaatctccgattcttaatttacgggttaaccgcgataaaaacttgctgtaaagcgggtttaagaaagatggttccgtctgttttacagaaacagaatccggcttattaatccctttttttaaggtattataaaa Find is-nt database================================================ Query_seq: TDE1347:TDE1348|TDE1347:TDE1348:hypothetical protein:TPR domain protein:->->:1388093..1388472 380 aaagaataaataattttgggattaagggaaccgctgcatttgcagaggaaagtccggactccttcggaaacgatgccggctaacggccggggaacggaaattaaagtttccgtttacagacagtgcaacagaaagtaaaccgccgcattttgcggtaagggtgaaagggcggggtaagagcccaccgcgttttcggtaacggaaacggcaatgtaaacctcatcgggagcaaggttaagcagtaaagaatctccgattcttaatttacgggttaaccgcgataaaaacttgctgtaaagcgggtttaagaaagatggttccgtctgttttacagaaacagaatccggcttattaatccctttttttaaggtattataaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE1347:TDE1348|TDE1347:TDE1348:hypothetical protein:TPR domain protein:->->:1388093..1388472 380 aaagaataaataattttgggattaagggaaccgctgcatttgcagaggaaagtccggactccttcggaaacgatgccggctaacggccggggaacggaaattaaagtttccgtttacagacagtgcaacagaaagtaaaccgccgcattttgcggtaagggtgaaagggcggggtaagagcccaccgcgttttcggtaacggaaacggcaatgtaaacctcatcgggagcaaggttaagcagtaaagaatctccgattcttaatttacgggttaaccgcgataaaaacttgctgtaaagcgggtttaagaaagatggttccgtctgttttacagaaacagaatccggcttattaatccctttttttaaggtattataaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE1347:TDE1348|TDE1347:TDE1348:hypothetical protein:TPR domain protein:->->:1388093..1388472 380 aaagaataaataattttgggattaagggaaccgctgcatttgcagaggaaagtccggactccttcggaaacgatgccggctaacggccggggaacggaaattaaagtttccgtttacagacagtgcaacagaaagtaaaccgccgcattttgcggtaagggtgaaagggcggggtaagagcccaccgcgttttcggtaacggaaacggcaatgtaaacctcatcgggagcaaggttaagcagtaaagaatctccgattcttaatttacgggttaaccgcgataaaaacttgctgtaaagcgggtttaagaaagatggttccgtctgttttacagaaacagaatccggcttattaatccctttttttaaggtattataaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aaagaataaataattttgggattaagggaaccgctgcatttgcagaggaaagtccggactccttcggaaacgatgccggctaacggccggggaacggaaattaaagtttccgtttacagacagtgcaacagaaagtaaaccgccgcattttgcggtaagggtgaaagggcggggtaagagcccaccgcgttttcggtaacggaaacggcaatgtaaacctcatcgggagcaaggttaagcagtaaagaatctccgattcttaatttacgggttaaccgcgataaaaacttgctgtaaagcgggtttaagaaagatggttccgtctgttttacagaaacagaatccggcttattaatccctttttttaaggtattataaaa Predict ORF larger than 30AA ================================================ Protein_Len: 42 Strand: + Start: 10 End: 135 ......... M I L G L R E P L H L Q R K V R T P S E T M P A N G R G T E I K V S V Y R Q C N R K ..................................................................................................................................................................................................................................................... Protein_Len: 53 Strand: + Start: 38 End: 196 ..................................... M C R G K S G L L R K R C R L T A G E R K L K F P F T D S A T E S K P P H F A V R V K G R G K S P P R F R ........................................................................................................................................................................................ Protein_Len: 30 Strand: + Start: 263 End: 352 ...................................................................................................................................................................................................................................................................... M Y G L T A I K T C C K A G L R K M V P S V L Q K Q N P A Y ............................ Protein_Len: 60 Strand: - Start: 117 End: 356 .................................................................................................................... S G V A N E T V S V A I Y V E D P A L N L L L S D G I R L K R T L R S L F K S Y L P N L F S P E T Q K V S V S D P K N M ........................ Protein_Len: 49 Strand: - Start: 104 End: 250 ....................................................................................................... L K R K C V T C C F T F R R M K R Y P H F P P T L A W R T K P L P F P L T F R M P L L T L C Y L M .................................................................................................................................. Protein_Len: 33 Strand: - Start: 25 End: 123 ........................ P F R Q M Q L P F D P S R R F R H R S V A P S R F N F N G N V S M ................................................................................................................................................................................................................................................................. Protein_Len: 33 Strand: - Start: 3 End: 101 .. S Y I I K P N L S G S C K C L F T R V G E S V I G A L P R P V S M ....................................................................................................................................................................................................................................................................................... aaagaataaataattttgggattaagggaaccgctgcatttgcagaggaaagtccggactccttcggaaacgatgccggctaacggccggggaacggaaattaaagtttccgtttacagacagtgcaacagaaagtaaaccgccgcattttgcggtaagggtgaaagggcggggtaagagcccaccgcgttttcggtaacggaaacggcaatgtaaacctcatcgggagcaaggttaagcagtaaagaatctccgattcttaatttacgggttaaccgcgataaaaacttgctgtaaagcgggtttaagaaagatggttccgtctgttttacagaaacagaatccggcttattaatccctttttttaaggtattataaaa 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================================================ aaagaataaataattttgggattaagggaaccgctgcatttgcagaggaaagtccggactccttcggaaacgatgccggctaacggccggggaacggaaattaaagtttccgtttacagacagtgcaacagaaagtaaaccgccgcattttgcggtaagggtgaaagggcggggtaagagcccaccgcgttttcggtaacggaaacggcaatgtaaacctcatcgggagcaaggttaagcagtaaagaatctccgattcttaatttacgggttaaccgcgataaaaacttgctgtaaagcgggtttaagaaagatggttccgtctgttttacagaaacagaatccggcttattaatccctttttttaaggtattataaaa Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE1347:TDE1348|TDE1347:TDE1348:hypothetical protein:TPR domain protein:->->:1388093..1388472 380 aaagaataaataattttgggattaagggaaccgctgcatttgcagaggaaagtccggactccttcggaaacgatgccggctaacggccggggaacggaaattaaagtttccgtttacagacagtgcaacagaaagtaaaccgccgcattttgcggtaagggtgaaagggcggggtaagagcccaccgcgttttcggtaacggaaacggcaatgtaaacctcatcgggagcaaggttaagcagtaaagaatctccgattcttaatttacgggttaaccgcgataaaaacttgctgtaaagcgggtttaagaaagatggttccgtctgttttacagaaacagaatccggcttattaatccctttttttaaggtattataaaa Intra-Species Hit: Count: 1 Min: 1 Max: 359 Len: 359 Subject: NC_002967_TDE1347_TDE1348|hypothetical protein:TPR domain protein|POSITIVE:POSITIVE|[1388093,1388472]|380 HSP 1 e-value: 0.0 bit: 712.0 Len: 359 Query Start:1 Query End:359 Subject Strand: POSITIVE Subject Start: 1 Subject End: 359 aaagaataaataattttgggattaagggaaccgctgcatttgcagaggaaagtccggactccttcggaaacgatgccggctaacggccggggaacggaaattaaagtttccgtttacagacagtgcaacagaaagtaaaccgccgcattttgcggtaagggtgaaagggcggggtaagagcccaccgcgttttcggtaacggaaacggcaatgtaaacctcatcgggagcaaggttaagcagtaaagaatctccgattcttaatttacgggttaaccgcgataaaaacttgctgtaaagcgggtttaagaaagatggttccgtctgttttacagaaacagaatccggcttattaatccc..................... aaagaataaataattttgggattaagggaaccgctgcatttgcagaggaaagtccggactccttcggaaacgatgccggctaacggccggggaacggaaattaaagtttccgtttacagacagtgcaacagaaagtaaaccgccgcattttgcggtaagggtgaaagggcggggtaagagcccaccgcgttttcggtaacggaaacggcaatgtaaacctcatcgggagcaaggttaagcagtaaagaatctccgattcttaatttacgggttaaccgcgataaaaacttgctgtaaagcgggtttaagaaagatggttccgtctgttttacagaaacagaatccggcttattaatccc..................... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAGAAUAAAUAAUUUUGGGAUUAAGGGAACCGCUGCAUUUGCAGAGGAAAGUCCGGACUCCUUCGGAAACGAUGCCGGCUAACGGCCGGGGAACGGAAAUUAAAGUUUCCGUUUACAGACAGUGCAACAGAAAGUAAACCGCCGCAUUUUGCGGUAAGGGUGAAAGGGCGGGGUAAGAGCCCACCGCGUUUUCGGUAACGGAAACGGCAAUGUAAACCUCAUCGGGAGCAAGGUUAAGCAGUAAAGAAUCUCCGAUUCUUAAUUUACGGGUUAACCGCGAUAAAAACUUGCUGUAAAGCGGGUUUAAGAAAGAUGGUUCCGUCUGUUUUACAGAAACAGAAUCCGGCUUAUUAAUCCC .................((((((((.....((.((((....)))).)).(((.(((((.((..(((....)))..(((((.....))))).((((((((((....)))))))))).......(((.((((((.........(((((.....)))))...(((((..((...((((....)))).)).((((((((....))))))))............))))).(((((..((((((.(.((((((((((...))))))....)))).).)))))).......(((((((((....)))))))))..........))))).)))))).))).......)).)))))))).)))))))) (-125.60) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GGGAUUAAUAAGCCGGAUUCUGUUUCUGUAAAACAGACGGAACCAUCUUUCUUAAACCCGCUUUACAGCAAGUUUUUAUCGCGGUUAACCCGUAAAUUAAGAAUCGGAGAUUCUUUACUGCUUAACCUUGCUCCCGAUGAGGUUUACAUUGCCGUUUCCGUUACCGAAAACGCGGUGGGCUCUUACCCCGCCCUUUCACCCUUACCGCAAAAUGCGGCGGUUUACUUUCUGUUGCACUGUCUGUAAACGGAAACUUUAAUUUCCGUUCCCCGGCCGUUAGCCGGCAUCGUUUCCGAAGGAGUCCGGACUUUCCUCUGCAAAUGCAGCGGUUCCCUUAAUCCCAAAAUUAUUUAUUCUUU ((((((((.((((((((((((...((((.....))))(((((.(....(((((((....(((....)))...........((((.....))))...))))))).((((((((.......((..((((((.........))))))......)).(((((((((((.((....(((((((((.........))))..........)))))....((((((((........))))))))...)).)).)))))))))...))))))))....(((((.....)))))....).)))))..))))))))).))).((.((((....)))).)).....))))))))................. (-111.20) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 394 92 51 72 22 NC_002967:TDE1894|5end_ferredoxin_1914113..1914343_POSITIVE 393 98 51 217 162 NC_002967:TDE1846|5end_hypothetical_protein_1875426..1875656_NEGATIVE 392 189 142 163 118 NC_002967:TDE2129|5end_hypothetical_protein_2161463..2161693_POSITIVE 391 159 111 190 131 NC_002967:TDE0946|5end_hypothetical_protein_968212..968442_POSITIVE 390 98 51 58 6 NC_002967:TDE1737|5end_hypothetical_protein_1790133..1790363_POSITIVE 390 80 33 68 2 NC_002967:TDE0142|5end_hypothetical_protein_164074..164304_NEGATIVE 388 78 31 167 113 NC_002967:TDE1005|5end_hypothetical_protein_1030206..1030436_POSITIVE 387 120 74 208 148 NC_002967:TDE0711|5end_hypothetical_protein_746181..746411_NEGATIVE 380 179 139 51 8 NC_002967:TDE2238|5end_hypothetical_protein_2276337..2276567_POSITIVE 378 208 162 230 191 NC_002967:TDE1534|5end_hypothetical_protein_1579128..1579358_NEGATIVE 374 230 184 59 15 NC_002967:TDE2209|5end_CarB_family_protein_2247589..2247819_POSITIVE 372 226 181 150 80 NC_002967:TDE2740|5end_type_I_restriction-modification_system,_S_subunit,_truncation_2795202..2795432_POSITIVE 367 89 43 208 160 NC_002967:TDE1590|5end_aminotransferase,_DegT/DnrJ/EryC1/StrS_family_1637516..1637746_POSITIVE 365 87 42 58 1 NC_002967:TDE2574|5end_conserved_hypothetical_protein_TIGR00650_2600376..2600606_POSITIVE 358 56 16 183 147 NC_002967:TDE1018|5end_hypothetical_protein_1049227..1049457_POSITIVE 357 78 31 69 15 NC_002967:TDE1384|5end_cadmium-translocating_P-type_ATPase_1422765..1422995_POSITIVE 356 190 141 223 166 NC_002967:TDE2622|5end_ABC_transporter,_ATP-binding_protein_2663590..2663820_NEGATIVE 356 179 138 181 134 NC_002967:TDE2100|5end_hypothetical_protein_2125370..2125600_POSITIVE 354 230 182 181 120 NC_002967:TDE2632|5end_peptide_ABC_transporter,_ATP-binding_protein,_putative_2672650..2672880_POSITIVE 354 96 51 199 146 NC_002967:TDE2268|5end_hypothetical_protein_2304959..2305189_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 379 230 184 136 78 NC_002967:TDE2734|3end_hypothetical_protein_2789861..2790011_POSITIVE 371 90 50 141 93 NC_002967:TDE2423|3end_ribosomal_protein_L10_2453417..2453567_NEGATIVE 370 209 162 79 26 NC_002967:TDE2242|3end_antigen,_putative_2279569..2279719_NEGATIVE 369 197 156 68 14 NC_002967:TDE0239|3end_glycine_reductase_complex_protein_GrdD_271828..271978_NEGATIVE 359 77 31 146 110 NC_002967:TDE2527|3end_hypothetical_protein_2555449..2555599_NEGATIVE 358 56 16 87 51 NC_002967:TDE1017|3end_exodeoxyribonuclease_VII,_large_subunit_1049211..1049361_POSITIVE 357 186 143 83 28 NC_002967:TDE1913|3end_hypothetical_protein_1930897..1931047_POSITIVE 357 188 141 51 4 NC_002967:TDE1739|3end_femAB_family_protein_1792657..1792807_POSITIVE 357 78 31 75 21 NC_002967:TDE1383|3end_hypothetical_protein_1422851..1423001_POSITIVE 355 129 84 79 28 NC_002967:TDE2210|3end_hypothetical_protein_2249394..2249544_NEGATIVE 354 87 45 61 8 NC_002967:TDE2573|3end_glucose-6-phosphate_isomerase_2600459..2600609_POSITIVE 354 187 141 111 43 NC_002967:TDE1892|3end_hypothetical_protein_1912237..1912387_POSITIVE 349 189 141 127 74 NC_002967:TDE0141|3end_hypothetical_protein_164065..164215_POSITIVE 348 97 52 63 6 NC_002967:TDE0143|3end_thiamine_ABC_transporter,_thiamine-binding_protein_165103..165253_POSITIVE 343 74 32 54 2 NC_002967:TDE2763|3end_flagellar_motor_switch_protein_2817737..2817887_NEGATIVE 343 236 191 121 62 NC_002967:TDE2437|3end_cyclic_nucleotide_binding_domain_protein_2467418..2467568_NEGATIVE 341 175 138 65 27 NC_002967:TDE2328|3end_efflux_pump_component_MtrF_2366364..2366514_POSITIVE 338 179 137 56 28 NC_002967:TDE1855|3end_hypothetical_protein_1883213..1883363_POSITIVE 337 213 172 145 97 NC_002967:TDE0050|3end_RNA_methyltransferase,_TrmH_family_59283..59433_NEGATIVE 333 77 31 57 2 NC_002967:TDE1897|3end_phosphoribosylglycinamide_formyltransferase_1917525..1917675_NEGATIVE