Origin IGS: ccgatttccggacagtttgccatcgttttttttctaaatctgcatatctaacaaataatcaactgtttttaatcccaaaaataatacattacggtcaagaaaaatcacccatggataacttttaaatatatttaacccttttgggatcgtatcctatctacagaaaaagtgattgtgctttatccgcaaaagagtttgatcggtgcatcatgcaaataatcgagtcattggtattcttttcaatcatctgctgtgtaaagaatataaaaaaagccattctcgactagttttttccccagtctgtcaagaaaaaaaagcaatgtatcgatatgatcgctcccatgattgggaggaacaaaaaaattgtacctttgcgcaggtaaagaatattcgg .........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 ccgaatattctttacctgcgcaaaggtacaatttttttgttcctcccaatcatgggagcgatcatatcgatacattgcttttttttcttgacagactggggaaaaaactagtcgagaatggctttttttatattctttacacagcagatgattgaaaagaataccaatgactcgattatttgcatgatgcaccgatcaaactcttttgcggataaagcacaatcactttttctgtagataggatacgatcccaaaagggttaaatatatttaaaagttatccatgggtgatttttcttgaccgtaatgtattatttttgggattaaaaacagttgattatttgttagatatgcagatttagaaaaaaaacgatggcaaactgtccggaaatcgg Mask Tandem Repeat Region ================================================ ccgatttccggacagtttgccatcgttttttttctaaatctgcatatctaacaaataatcaactgtttttaatcccaaaaataatacattacggtcaagaaaaatcacccatggataacttttaaatatatttaacccttttgggatcgtatcctatctacagaaaaagtgattgtgctttatccgcaaaagagtttgatcggtgcatcatgcaaataatcgagtcattggtattcttttcaatcatctgctgtgtaaagaatataaaaaaagccattctcgactagttttttccccagtctgtcaagaaaaaaaagcaatgtatcgatatgatcgctcccatgattgggaggaacaaaaaaattgtacctttgcgcaggtaaagaatattcgg Find is-nt database================================================ Query_seq: TF1209:TF1210|TF1209:TF1210:RNA polymerase ECF-type sigma factor:conserved hypothetical protein:->->:1295441..1295834 394 ccgatttccggacagtttgccatcgttttttttctaaatctgcatatctaacaaataatcaactgtttttaatcccaaaaataatacattacggtcaagaaaaatcacccatggataacttttaaatatatttaacccttttgggatcgtatcctatctacagaaaaagtgattgtgctttatccgcaaaagagtttgatcggtgcatcatgcaaataatcgagtcattggtattcttttcaatcatctgctgtgtaaagaatataaaaaaagccattctcgactagttttttccccagtctgtcaagaaaaaaaagcaatgtatcgatatgatcgctcccatgattgggaggaacaaaaaaattgtacctttgcgcaggtaaagaatattcgg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF1209:TF1210|TF1209:TF1210:RNA polymerase ECF-type sigma factor:conserved hypothetical protein:->->:1295441..1295834 394 ccgatttccggacagtttgccatcgttttttttctaaatctgcatatctaacaaataatcaactgtttttaatcccaaaaataatacattacggtcaagaaaaatcacccatggataacttttaaatatatttaacccttttgggatcgtatcctatctacagaaaaagtgattgtgctttatccgcaaaagagtttgatcggtgcatcatgcaaataatcgagtcattggtattcttttcaatcatctgctgtgtaaagaatataaaaaaagccattctcgactagttttttccccagtctgtcaagaaaaaaaagcaatgtatcgatatgatcgctcccatgattgggaggaacaaaaaaattgtacctttgcgcaggtaaagaatattcgg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF1209:TF1210|TF1209:TF1210:RNA polymerase ECF-type sigma factor:conserved hypothetical protein:->->:1295441..1295834 394 ccgatttccggacagtttgccatcgttttttttctaaatctgcatatctaacaaataatcaactgtttttaatcccaaaaataatacattacggtcaagaaaaatcacccatggataacttttaaatatatttaacccttttgggatcgtatcctatctacagaaaaagtgattgtgctttatccgcaaaagagtttgatcggtgcatcatgcaaataatcgagtcattggtattcttttcaatcatctgctgtgtaaagaatataaaaaaagccattctcgactagttttttccccagtctgtcaagaaaaaaaagcaatgtatcgatatgatcgctcccatgattgggaggaacaaaaaaattgtacctttgcgcaggtaaagaatattcgg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ccgatttccggacagtttgccatcgttttttttctaaatctgcatatctaacaaataatcaactgtttttaatcccaaaaataatacattacggtcaagaaaaatcacccatggataacttttaaatatatttaacccttttgggatcgtatcctatctacagaaaaagtgattgtgctttatccgcaaaagagtttgatcggtgcatcatgcaaataatcgagtcattggtattcttttcaatcatctgctgtgtaaagaatataaaaaaagccattctcgactagttttttccccagtctgtcaagaaaaaaaagcaatgtatcgatatgatcgctcccatgattgggaggaacaaaaaaattgtacctttgcgcaggtaaagaatattcgg Predict ORF larger than 30AA ================================================ Protein_Len: 53 Strand: + Start: 126 End: 284 ............................................................................................................................. M Y L T L L G S Y P I Y R K S D C A L S A K E F D R C I M Q I I E S L V F F S I I C C V K N I K K A I L D .............................................................................................................. Protein_Len: 60 Strand: + Start: 203 End: 394 .......................................................................................................................................................................................................... M H H A N N R V I G I L F N H L L C K E Y K K S H S R L V F S P V C Q E K K A M Y R Y D R S H D W E E Q K N C T F A Q V Protein_Len: 34 Strand: - Start: 287 End: 388 .............................................................................................................................................................................................................................................................................................. N K G W D T L F F F C H I S I I A G M I P L F L F I T G K R L Y L M ...... Protein_Len: 39 Strand: - Start: 161 End: 277 ................................................................................................................................................................ L F L S Q A K D A F S N S R H M M C I I S D N T N K E I M Q Q T F F I F F A M ..................................................................................................................... Protein_Len: 37 Strand: - Start: 37 End: 147 .................................... I Q M D L L Y D V T K L G L F L V N R D L F I V W P Y S K F I N L G K P M ....................................................................................................................................................................................................................................................... ccgatttccggacagtttgccatcgttttttttctaaatctgcatatctaacaaataatcaactgtttttaatcccaaaaataatacattacggtcaagaaaaatcacccatggataacttttaaatatatttaacccttttgggatcgtatcctatctacagaaaaagtgattgtgctttatccgcaaaagagtttgatcggtgcatcatgcaaataatcgagtcattggtattcttttcaatcatctgctgtgtaaagaatataaaaaaagccattctcgactagttttttccccagtctgtcaagaaaaaaaagcaatgtatcgatatgatcgctcccatgattgggaggaacaaaaaaattgtacctttgcgcaggtaaagaatattcgg 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================================================ ccgatttccggacagtttgccatcgttttttttctaaatctgcatatctaacaaataatcaactgtttttaatcccaaaaataatacattacggtcaagaaaaatcacccatggataacttttaaatatatttaacccttttgggatcgtatcctatctacagaaaaagtgattgtgctttatccgcaaaagagtttgatcggtgcatcatgcaaataatcgagtcattggtattcttttcaatcatctgctgtgtaaagaatataaaaaaagccattctcgactagttttttccccagtctgtcaagaaaaaaaagcaatgtatcgatatgatcgctcccatgattgggaggaacaaaaaaattgtacctttgcgcaggtaaagaatattcgg Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 50 HP_score: -3.1 Tail_Score: -3.54424 Start: 352 End: 370 Full_Region: CTCCCATGATTGGGA GGAACAA AAAAA TTGTACC TTTGCGCAGGTAAAG ...............................................................................................................................................................................................................................................................................................................................................................GGAACAAAAAAATTGTACC........................ Find igs database================================================ Query_seq: TF1209:TF1210|TF1209:TF1210:RNA polymerase ECF-type sigma factor:conserved hypothetical protein:->->:1295441..1295834 394 ccgatttccggacagtttgccatcgttttttttctaaatctgcatatctaacaaataatcaactgtttttaatcccaaaaataatacattacggtcaagaaaaatcacccatggataacttttaaatatatttaacccttttgggatcgtatcctatctacagaaaaagtgattgtgctttatccgcaaaagagtttgatcggtgcatcatgcaaataatcgagtcattggtattcttttcaatcatctgctgtgtaaagaatataaaaaaagccattctcgactagttttttccccagtctgtcaagaaaaaaaagcaatgtatcgatatgatcgctcccatgattgggaggaacaaaaaaattgtacctttgcgcaggtaaagaatattcgg Intra-Species Hit: Count: 1 Min: 1 Max: 394 Len: 394 Subject: tfor_TF1209_TF1210|RNA polymerase ECF-type sigma factor:conserved hypothetical protein|POSITIVE:POSITIVE|[1295441,1295834]|394 HSP 1 e-value: 1.0E-171 bit: 603.0 Len: 394 Query Start:1 Query End:394 Subject Strand: POSITIVE Subject Start: 1 Subject End: 394 ccgatttccggacagtttgccatcgnnnnnnnnctaaatctgcatatctaacaaataatcaactgtttttaatcccaaaaataatacattacggtcaagaaaaatcacccatggataacttttaaatatatttaacccttttgggatcgtatcctatctacagaaaaagtgattgtgctttatccgcaaaagagtttgatcggtgcatcatgcaaataatcgagtcattggtattcttttcaatcatctgctgtgtaaagaatatnnnnnnngccattctcgactagttttttccccagtctgtcaagnnnnnnnngcaatgtatcgatatgatcgctcccatgattgggaggaacnnnnnnnttgtacctttgcgcaggtaaagaatattcgg ccgatttccggacagtttgccatcgttttttttctaaatctgcatatctaacaaataatcaactgtttttaatcccaaaaataatacattacggtcaagaaaaatcacccatggataacttttaaatatatttaacccttttgggatcgtatcctatctacagaaaaagtgattgtgctttatccgcaaaagagtttgatcggtgcatcatgcaaataatcgagtcattggtattcttttcaatcatctgctgtgtaaagaatataaaaaaagccattctcgactagttttttccccagtctgtcaagaaaaaaaagcaatgtatcgatatgatcgctcccatgattgggaggaacaaaaaaattgtacctttgcgcaggtaaagaatattcgg Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CCGAUUUCCGGACAGUUUGCCAUCGUUUUUUUUCUAAAUCUGCAUAUCUAACAAAUAAUCAACUGUUUUUAAUCCCAAAAAUAAUACAUUACGGUCAAGAAAAAUCACCCAUGGAUAACUUUUAAAUAUAUUUAACCCUUUUGGGAUCGUAUCCUAUCUACAGAAAAAGUGAUUGUGCUUUAUCCGCAAAAGAGUUUGAUCGGUGCAUCAUGCAAAUAAUCGAGUCAUUGGUAUUCUUUUCAAUCAUCUGCUGUGUAAAGAAUAUAAAAAAAGCCAUUCUCGACUAGUUUUUUCCCCAGUCUGUCAAGAAAAAAAAGCAAUGUAUCGAUAUGAUCGCUCCCAUGAUUGGGAGGAACAAAAAAAUUGUACCUUUGCGCAGGUAAAGAAUAUUCGG ((((.....((.(.....)))..........((((..((((((........(((((..((...(((((((......)))))))........(((..(((...((((((....(((((....(((((....)))))(((....)))....)))))..((....))....))))))...)))...))).....)))))))...(((((((((((((.....(((((....(((((((((((.((..(....)...)).))))))).........))))..)))))...(((((((......(((....)))..)))))))..))))).))..((.((.((((((....)))))))).)).......)))))).....))))))..))))...)))) (-79.20) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CCGAAUAUUCUUUACCUGCGCAAAGGUACAAUUUUUUUGUUCCUCCCAAUCAUGGGAGCGAUCAUAUCGAUACAUUGCUUUUUUUUCUUGACAGACUGGGGAAAAAACUAGUCGAGAAUGGCUUUUUUUAUAUUCUUUACACAGCAGAUGAUUGAAAAGAAUACCAAUGACUCGAUUAUUUGCAUGAUGCACCGAUCAAACUCUUUUGCGGAUAAAGCACAAUCACUUUUUCUGUAGAUAGGAUACGAUCCCAAAAGGGUUAAAUAUAUUUAAAAGUUAUCCAUGGGUGAUUUUUCUUGACCGUAAUGUAUUAUUUUUGGGAUUAAAAACAGUUGAUUAUUUGUUAGAUAUGCAGAUUUAGAAAAAAAACGAUGGCAAACUGUCCGGAAAUCGG ((((...((((.(((((......))))).........((.((((((((....)))))).)).))........(((((.((((((((((.((..((((((........)))))).((((((..........)))))).......((((((((((((................))))))))))))....((((...(((...((..((((((((.((((........)))).))))))))..))....(((((((((((.....((((((((.((((((((((....)))))))))).........)))))))).)))))))))))...(((((........))))).))).))))..)).)))))))))))))))...........)))).)))) (-94.89) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 346 379 335 154 114 tfor:TF2008|5end_DNA_polymerase_I_2159302..2159532_POSITIVE 343 227 185 74 22 tfor:TF0607|5end_DnaK_suppressor_protein_637441..637671_POSITIVE 320 378 335 114 70 tfor:TF0394|5end_oxaloacetate_decarboxylase,_alpha_subunit_(pyruvate_carboxylase,_C-terminal_domain)_413268..413498_POSITIVE 317 378 331 100 42 tfor:TF2815|5end_meso-diaminopimelate_D-dehydrogenase_3005429..3005659_POSITIVE 313 189 143 190 139 tfor:TF1981|5end_mannose-6-phosphate_isomerase_2130896..2131126_POSITIVE 308 213 179 172 145 tfor:TF2926|5end_glycine_hydroxymethyltransferase_3128070..3128300_POSITIVE 304 355 317 58 14 tfor:TF0680|5end_tail-specific_protease_721393..721623_POSITIVE 299 352 316 52 10 tfor:TF2457|5end_ABC_transporter,_permease_component,_zinc-binding_protein_2633147..2633377_POSITIVE 296 213 174 203 173 tfor:TF2348|5end_outer_membrane_protein,_possibly_involved_in_nutrient_binding_2511088..2511318_POSITIVE 293 24 1 42 19 tfor:TF0496|5end_conserved_hypothetical_protein_522332..522562_POSITIVE 288 341 301 49 2 tfor:TF0409|5end_conserved_hypothetical_protein_426240..426470_POSITIVE 284 213 182 28 1 tfor:TF1935|5end_ATP-dependent_RNA_helicase,_DEAD/DEAH-related_helicase_2082002..2082232_POSITIVE 281 189 143 189 139 tfor:TF1825|5end_mannose-6-phosphate_isomerase_1973578..1973808_POSITIVE 280 206 161 57 9 tfor:TF3076|5end_outer_membrane_protein,_TonB_dependent_receptor_3302785..3303015_POSITIVE 280 187 141 63 16 tfor:TF2324|5end_conserved_hypothetical_protein;_possible_cobalamin_adenosyltransferase_2483714..2483944_POSITIVE 279 349 316 203 157 tfor:TF2307|5end_two-component_system_sensor_histidine_kinase/response_2462618..2462848_POSITIVE 278 356 316 214 172 tfor:TF0242|5end_conserved_hypothetical_protein_272439..272669_POSITIVE 275 213 175 163 122 tfor:TF1574|5end_two-component_system_response_regulator_1681807..1682037_POSITIVE 274 230 183 75 29 tfor:TF0185|5end_4-alpha-glucanotransferase_(amylomaltase)_196486..196716_POSITIVE 272 309 271 187 137 tfor:TF2874|5end_conserved_hypothetical_protein_3064920..3065150_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 346 379 335 99 59 tfor:TF2007|3end_uracil_phosphoribosyltransferase_2159327..2159477_POSITIVE 343 227 185 57 5 tfor:TF0606|3end_signal_peptidase_II_637504..637654_POSITIVE 313 189 143 74 23 tfor:TF1980|3end_conserved_hypothetical_protein_2130860..2131010_POSITIVE 308 213 179 132 105 tfor:TF2925|3end_beta-N-acetylglucosaminidase_3128110..3128260_POSITIVE 304 355 317 74 30 tfor:TF0679|3end_hypothetical_protein_721489..721639_POSITIVE 296 213 174 127 97 tfor:TF2347|3end_outer_membrane_protein,_TonB_dependent_receptor_2511092..2511242_POSITIVE 288 341 301 53 6 tfor:TF0408|3end_possible_gliding_motility-related_lipoprotein_426324..426474_POSITIVE 286 230 181 109 56 tfor:TF1761|3end_hypothetical_protein_1899579..1899729_POSITIVE 281 377 335 62 21 tfor:TF2583|3end_possible_ABC_transporter,__permease_component_2751026..2751176_POSITIVE 280 187 141 54 7 tfor:TF2322|3end_conserved_hypothetical_protein;_possible_lipoprotein_2483785..2483935_POSITIVE 274 230 183 76 30 tfor:TF0183|3end_conserved_hypothetical_protein_196567..196717_POSITIVE 268 243 202 70 22 tfor:TF2101|3end_hypothetical_protein_2274537..2274687_POSITIVE 268 50 2 114 58 tfor:TF0242|3end_conserved_hypothetical_protein_274069..274219_POSITIVE 266 354 317 100 64 tfor:TF2078|3end_dehydrogenase_2245471..2245621_POSITIVE 264 303 271 141 103 tfor:TF2873|3end_conserved_hypothetical_protein_3064966..3065116_POSITIVE 264 228 185 41 4 tfor:TF0522|3end_hypothetical_protein_547873..548023_POSITIVE 264 228 185 63 26 tfor:TF0521|3end_hypothetical_protein_547895..548045_POSITIVE 261 43 1 51 2 tfor:TF1068|3end_conserved_hypothetical_protein;_possible_N-acetylglucosamine_kinase_1138964..1139114_POSITIVE 261 355 321 55 27 tfor:TF0632|3end_hypothetical_protein_668151..668301_POSITIVE 258 348 315 58 26 tfor:TF0230|3end_hydrolase,_haloacid_dehalogenase-like_family_257862..258012_POSITIVE