Origin IGS: tagcttttcaagtgtttgttttttttagttattgttgctttgcaaatgtgatgttttgattgtcaatcagaggttgacacaagatgtttaattgaatatcgggaatctttatcttgtacagagcataggattcccgattttgtcattcatattgcttctgttttgcagatcgatcattttaagacagagaactatacggattttatgcgtttgcatactgtgcgtggtgaacaccggtatgttaagcgcgatagatggaattttttttgcatctgatcgaaaacgcttctatctttgtgcgtttattttttatattttttataatcgtgttgattgcggctcttgtgcgtcaggcagtagagatgttgtccaccacaatataagcatattgcctgcatttcgattgtcaaccgataaataaatgatcaaaacatagaaaaggacgatggtcag .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9 ctgaccatcgtccttttctatgttttgatcatttatttatcggttgacaatcgaaatgcaggcaatatgcttatattgtggtggacaacatctctactgcctgacgcacaagagccgcaatcaacacgattataaaaaatataaaaaataaacgcacaaagatagaagcgttttcgatcagatgcaaaaaaaattccatctatcgcgcttaacataccggtgttcaccacgcacagtatgcaaacgcataaaatccgtatagttctctgtcttaaaatgatcgatctgcaaaacagaagcaatatgaatgacaaaatcgggaatcctatgctctgtacaagataaagattcccgatattcaattaaacatcttgtgtcaacctctgattgacaatcaaaacatcacatttgcaaagcaacaataactaaaaaaaacaaacacttgaaaagcta Mask Tandem Repeat Region ================================================ tagcttttcaagtgtttgttttttttagttattgttgctttgcaaatgtgatgttttgattgtcaatcagaggttgacacaagatgtttaattgaatatcgggaatctttatcttgtacagagcataggattcccgattttgtcattcatattgcttctgttttgcagatcgatcattttaagacagagaactatacggattttatgcgtttgcatactgtgcgtggtgaacaccggtatgttaagcgcgatagatggaattttttttgcatctgatcgaaaacgcttctatctttgtgcgtttattttttatattttttataatcgtgttgattgcggctcttgtgcgtcaggcagtagagatgttgtccaccacaatataagcatattgcctgcatttcgattgtcaaccgataaataaatgatcaaaacatagaaaaggacgatggtcag Find is-nt database================================================ Query_seq: TF2299:TF2300|TF2299:TF2300:hypothetical protein:conserved hypothetical protein:->->:2450308..2450760 453 tagcttttcaagtgtttgttttttttagttattgttgctttgcaaatgtgatgttttgattgtcaatcagaggttgacacaagatgtttaattgaatatcgggaatctttatcttgtacagagcataggattcccgattttgtcattcatattgcttctgttttgcagatcgatcattttaagacagagaactatacggattttatgcgtttgcatactgtgcgtggtgaacaccggtatgttaagcgcgatagatggaattttttttgcatctgatcgaaaacgcttctatctttgtgcgtttattttttatattttttataatcgtgttgattgcggctcttgtgcgtcaggcagtagagatgttgtccaccacaatataagcatattgcctgcatttcgattgtcaaccgataaataaatgatcaaaacatagaaaaggacgatggtcag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF2299:TF2300|TF2299:TF2300:hypothetical protein:conserved hypothetical protein:->->:2450308..2450760 453 tagcttttcaagtgtttgttttttttagttattgttgctttgcaaatgtgatgttttgattgtcaatcagaggttgacacaagatgtttaattgaatatcgggaatctttatcttgtacagagcataggattcccgattttgtcattcatattgcttctgttttgcagatcgatcattttaagacagagaactatacggattttatgcgtttgcatactgtgcgtggtgaacaccggtatgttaagcgcgatagatggaattttttttgcatctgatcgaaaacgcttctatctttgtgcgtttattttttatattttttataatcgtgttgattgcggctcttgtgcgtcaggcagtagagatgttgtccaccacaatataagcatattgcctgcatttcgattgtcaaccgataaataaatgatcaaaacatagaaaaggacgatggtcag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF2299:TF2300|TF2299:TF2300:hypothetical protein:conserved hypothetical protein:->->:2450308..2450760 453 tagcttttcaagtgtttgttttttttagttattgttgctttgcaaatgtgatgttttgattgtcaatcagaggttgacacaagatgtttaattgaatatcgggaatctttatcttgtacagagcataggattcccgattttgtcattcatattgcttctgttttgcagatcgatcattttaagacagagaactatacggattttatgcgtttgcatactgtgcgtggtgaacaccggtatgttaagcgcgatagatggaattttttttgcatctgatcgaaaacgcttctatctttgtgcgtttattttttatattttttataatcgtgttgattgcggctcttgtgcgtcaggcagtagagatgttgtccaccacaatataagcatattgcctgcatttcgattgtcaaccgataaataaatgatcaaaacatagaaaaggacgatggtcag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tagcttttcaagtgtttgttttttttagttattgttgctttgcaaatgtgatgttttgattgtcaatcagaggttgacacaagatgtttaattgaatatcgggaatctttatcttgtacagagcataggattcccgattttgtcattcatattgcttctgttttgcagatcgatcattttaagacagagaactatacggattttatgcgtttgcatactgtgcgtggtgaacaccggtatgttaagcgcgatagatggaattttttttgcatctgatcgaaaacgcttctatctttgtgcgtttattttttatattttttataatcgtgttgattgcggctcttgtgcgtcaggcagtagagatgttgtccaccacaatataagcatattgcctgcatttcgattgtcaaccgataaataaatgatcaaaacatagaaaaggacgatggtcag Predict ORF larger than 30AA ================================================ Protein_Len: 60 Strand: + Start: 91 End: 273 .......................................................................................... M E Y R E S L S C T E H R I P D F V I H I A S V L Q I D H F K T E N Y T D F M R L H T V R G E H R Y V K R D R W N F F C .................................................................................................................................................................................... Protein_Len: 42 Strand: + Start: 255 End: 380 .............................................................................................................................................................................................................................................................. M E F F L H L I E N A S I F V R L F F I F F I I V L I A A L V R Q A V E M L S T T I ......................................................................... Protein_Len: 60 Strand: + Start: 92 End: 418 ........................................................................................... M N I G N L Y L V Q S I G F P I L S F I L L L F C R S I I L R Q R T I R I L C V C I L C V V N T G M L S A I D G I F F A ................................... Protein_Len: 44 Strand: - Start: 322 End: 453 ................................................................................................................................................................................................................................................................................................................................. L R T S Q P E Q A D P L L S T T W W L I L M N G A N R N D V S L Y I I L V Y F L V I T M Protein_Len: 38 Strand: - Start: 306 End: 419 ................................................................................................................................................................................................................................................................................................................. K K Y K K Y D H Q N R S K H T L C Y L H Q G G C Y L C I A Q M E I T L R Y M .................................. Protein_Len: 30 Strand: - Start: 245 End: 334 .................................................................................................................................................................................................................................................... A R Y I S N K K C R I S F A E I K T R K N K I N K I I T N M ....................................................................................................................... Protein_Len: 50 Strand: - Start: 112 End: 261 ............................................................................................................... R T C L M P N G I K D N M N S R N Q L D I M K L C L V I R I K H T Q M S H T T F V P I N L A I S P M ................................................................................................................................................................................................ Protein_Len: 30 Strand: - Start: 32 End: 121 ............................... Q Q K A F T I N Q N D I L P Q C L I N L Q I D P I K I K Y M ............................................................................................................................................................................................................................................................................................................................................ tagcttttcaagtgtttgttttttttagttattgttgctttgcaaatgtgatgttttgattgtcaatcagaggttgacacaagatgtttaattgaatatcgggaatctttatcttgtacagagcataggattcccgattttgtcattcatattgcttctgttttgcagatcgatcattttaagacagagaactatacggattttatgcgtttgcatactgtgcgtggtgaacaccggtatgttaagcgcgatagatggaattttttttgcatctgatcgaaaacgcttctatctttgtgcgtttattttttatattttttataatcgtgttgattgcggctcttgtgcgtcaggcagtagagatgttgtccaccacaatataagcatattgcctgcatttcgattgtcaaccgataaataaatgatcaaaacatagaaaaggacgatggtcag 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================================================ tagcttttcaagtgtttgttttttttagttattgttgctttgcaaatgtgatgttttgattgtcaatcagaggttgacacaagatgtttaattgaatatcgggaatctttatcttgtacagagcataggattcccgattttgtcattcatattgcttctgttttgcagatcgatcattttaagacagagaactatacggattttatgcgtttgcatactgtgcgtggtgaacaccggtatgttaagcgcgatagatggaattttttttgcatctgatcgaaaacgcttctatctttgtgcgtttattttttatattttttataatcgtgttgattgcggctcttgtgcgtcaggcagtagagatgttgtccaccacaatataagcatattgcctgcatttcgattgtcaaccgataaataaatgatcaaaacatagaaaaggacgatggtcag Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 64 HP_score: -3.4 Tail_Score: -4.57209 Start: 99 End: 137 Full_Region: ATGTTTAATTGAATA TCGGGAATCTTTATCTT GTACA GAGCATAGGATTCCCGA TTTTGTCATTCATAT ..................................................................................................TCGGGAATCTTTATCTTGTACAGAGCATAGGATTCCCGA............................................................................................................................................................................................................................................................................................................................ Find igs database================================================ Query_seq: TF2299:TF2300|TF2299:TF2300:hypothetical protein:conserved hypothetical protein:->->:2450308..2450760 453 tagcttttcaagtgtttgttttttttagttattgttgctttgcaaatgtgatgttttgattgtcaatcagaggttgacacaagatgtttaattgaatatcgggaatctttatcttgtacagagcataggattcccgattttgtcattcatattgcttctgttttgcagatcgatcattttaagacagagaactatacggattttatgcgtttgcatactgtgcgtggtgaacaccggtatgttaagcgcgatagatggaattttttttgcatctgatcgaaaacgcttctatctttgtgcgtttattttttatattttttataatcgtgttgattgcggctcttgtgcgtcaggcagtagagatgttgtccaccacaatataagcatattgcctgcatttcgattgtcaaccgataaataaatgatcaaaacatagaaaaggacgatggtcag Intra-Species Hit: Count: 1 Min: 1 Max: 453 Len: 453 Subject: tfor_TF2299_TF2300|hypothetical protein:conserved hypothetical protein|POSITIVE:POSITIVE|[2450308,2450760]|453 HSP 1 e-value: 1.0E-141 bit: 502.0 Len: 301 Query Start:1 Query End:301 Subject Strand: POSITIVE Subject Start: 1 Subject End: 301 tagcttttcaagtgtttgnnnnnnnnagttattgttgctttgcaaatgtgatgttttgattgtcaatcagaggttgacacaagatgtttaattgaatatcgggaatctttatcttgtacagagcataggattcccgattttgtcattcatattgcttctgttttgcagatcgatcattttaagacagagaactatacggattttatgcgtttgcatactgtgcgtggtgaacaccggtatgttaagcgcgatagatggaannnnnnnngcatctgatcgaaaacgcttctatctttgtgcg........................................................................................................................................................ tagcttttcaagtgtttgttttttttagttattgttgctttgcaaatgtgatgttttgattgtcaatcagaggttgacacaagatgtttaattgaatatcgggaatctttatcttgtacagagcataggattcccgattttgtcattcatattgcttctgttttgcagatcgatcattttaagacagagaactatacggattttatgcgtttgcatactgtgcgtggtgaacaccggtatgttaagcgcgatagatggaattttttttgcatctgatcgaaaacgcttctatctttgtgcg........................................................................................................................................................ HSP 2 e-value: 2.0E-69 bit: 264.0 Len: 133 Query Start:321 Query End:453 Subject Strand: POSITIVE Subject Start: 321 Subject End: 453 ................................................................................................................................................................................................................................................................................................................................ataatcgtgttgattgcggctcttgtgcgtcaggcagtagagatgttgtccaccacaatataagcatattgcctgcatttcgattgtcaaccgataaataaatgatcaaaacatagaaaaggacgatggtcag ................................................................................................................................................................................................................................................................................................................................ataatcgtgttgattgcggctcttgtgcgtcaggcagtagagatgttgtccaccacaatataagcatattgcctgcatttcgattgtcaaccgataaataaatgatcaaaacatagaaaaggacgatggtcag Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAGCUUUUCAAGUGUUUGUUUUUUUUAGUUAUUGUUGCUUUGCAAAUGUGAUGUUUUGAUUGUCAAUCAGAGGUUGACACAAGAUGUUUAAUUGAAUAUCGGGAAUCUUUAUCUUGUACAGAGCAUAGGAUUCCCGAUUUUGUCAUUCAUAUUGCUUCUGUUUUGCAGAUCGAUCAUUUUAAGACAGAGAACUAUACGGAUUUUAUGCGUUUGCAUACUGUGCGUGGUGAACACCGGUAUGUUAAGCGCGAUAGAUGGAAUUUUUUUUGCAUCUGAUCGAAAACGCUUCUAUCUUUGUGCGUUUAUUUUUUAUAUUUUUUAUAAUCGUGUUGAUUGCGGCUCUUGUGCGUCAGGCAGUAGAGAUGUUGUCCACCACAAUAUAAGCAUAUUGCCUGCAUUUCGAUUGUCAACCGAUAAAUAAAUGAUCAAAACAUAGAAAAGGACGAUGGUCAG ...((((((.(((((((........(((((...........((((.(((((.((((((..(((((((.....))))))))))))).......(((..((((((((((((...(((.....)))...))))))))))))....))).))))))))).(((((((((.((((.....))))))))))))).)))))..(((.......((((((((((((((.(.((.....)).)))))))).)))))))..((((((.((......)).)))))).))).)))))))......((((..(((((((((.(((((.....)))))(((.((((((..(((.....((((...(((((((((..(((((((.....)))))))...).)))))))))))).)))...))))))))).)))))))))..)))).....))))))(((....))).. (-124.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUGACCAUCGUCCUUUUCUAUGUUUUGAUCAUUUAUUUAUCGGUUGACAAUCGAAAUGCAGGCAAUAUGCUUAUAUUGUGGUGGACAACAUCUCUACUGCCUGACGCACAAGAGCCGCAAUCAACACGAUUAUAAAAAAUAUAAAAAAUAAACGCACAAAGAUAGAAGCGUUUUCGAUCAGAUGCAAAAAAAAUUCCAUCUAUCGCGCUUAACAUACCGGUGUUCACCACGCACAGUAUGCAAACGCAUAAAAUCCGUAUAGUUCUCUGUCUUAAAAUGAUCGAUCUGCAAAACAGAAGCAAUAUGAAUGACAAAAUCGGGAAUCCUAUGCUCUGUACAAGAUAAAGAUUCCCGAUAUUCAAUUAAACAUCUUGUGUCAACCUCUGAUUGACAAUCAAAACAUCACAUUUGCAAAGCAACAAUAACUAAAAAAAACAAACACUUGAAAAGCUA ............((((((.((((((((((...(((.(((..(((((((..........(((((.....((.......)).(((((.......))))).)))))....((((((...((........(((((((......(((.....)))........((((((((.(((....((((.(((((.((......)).))))))))))))..(((((((.(((....)))........(((((....)))))......)))).))).))))))))...))))))).((((.....)))).))....(((((......((((((((((......(((.....)))....)))))))))))))))........)))))))))))))..))).)))..)))))))))).....((((...)))).........................))))))... (-97.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 375 376 336 165 124 tfor:TF2455|5end_conserved_hypothetical_protein;_possible_membrane_protein_2631959..2632189_POSITIVE 373 376 335 70 4 tfor:TF2237|5end_two-component_system_response_regulator_involved_in_CTn_2412494..2412724_POSITIVE 371 370 328 218 174 tfor:TF0545|5end_glucose-inhibited_division_protein_B_575756..575986_POSITIVE 356 269 224 68 21 tfor:TF2266|5end_transfer_region-related_protein,_TraQ_2434369..2434599_POSITIVE 353 249 207 204 155 tfor:TF0648|5end_possible_FHA_domain_protein_690068..690298_POSITIVE 350 370 324 228 175 tfor:TF2372|5end_acyl-(acyl-carrier-protein)-UDP-N-acetylglucosami_ne_acyltransferase_2537558..2537788_POSITIVE 349 259 213 98 57 tfor:TF2917|5end_conserved_hypothetical_protein_3112255..3112485_POSITIVE 345 250 202 78 17 tfor:TF0611|5end_lysine_decarboxylase_642750..642980_POSITIVE 341 369 324 92 27 tfor:TF1055|5end_hypothetical_protein_1119646..1119876_POSITIVE 340 370 325 61 15 tfor:TF2895|5end_hypothetical_protein_3083936..3084166_POSITIVE 338 370 325 77 21 tfor:TF0011|5end_conserved_hypothetical_protein_4685..4915_POSITIVE 337 249 207 55 4 tfor:TF0180|5end_carboxynorspermidine_decarboxylase_191267..191497_POSITIVE 336 366 324 64 18 tfor:TF1179|5end_two-component_sensor_histidine_kinase_1266057..1266287_POSITIVE 334 308 269 65 30 tfor:TF0093|5end_outer_membrane_protein,_TonB_dependent_receptor_100497..100727_POSITIVE 331 366 321 71 27 tfor:TF3043|5end_conserved_hypothetical_protein_3271925..3272155_POSITIVE 329 260 211 211 152 tfor:TF1004|5end_ABC_transporter,_ATP-binding_protein_1058861..1059091_POSITIVE 328 259 213 155 112 tfor:TF3108|5end_glutamine-hydrolyzing_carbamoyl-phosphate_synthase,_large_subunit_3338732..3338962_POSITIVE 328 229 183 82 35 tfor:TF2677|5end_aspartate_transaminase_2850809..2851039_POSITIVE 326 379 337 206 165 tfor:TF1887|5end_hypothetical_protein_2040301..2040531_POSITIVE 322 360 325 49 11 tfor:TF1819|5end_cation_efflux_system_AcrB/AcrD/AcrF_family;_ABC_transporter,_ATP-binding/permease_component_1958681..1958911_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 375 376 336 151 110 tfor:TF2454|3end_D-alanyl-D-alanine_dipeptidase_2632025..2632175_POSITIVE 373 376 335 74 8 tfor:TF2236|3end_two-component_system_histidine_kinase_involved_in_CTn_2412578..2412728_POSITIVE 338 370 325 102 46 tfor:TF0010|3end_conserved_hypothetical_protein_4790..4940_POSITIVE 336 366 324 55 9 tfor:TF1178|3end_sigma-54_dependent_DNA-binding_response_regulator_1266128..1266278_POSITIVE 336 250 203 61 1 tfor:TF0609|3end_conserved_hypothetical_protein_642813..642963_POSITIVE 334 308 269 37 2 tfor:TF0092|3end_outer_membrane_protein_100549..100699_POSITIVE 328 259 213 79 36 tfor:TF3107|3end_hypothetical_protein_3338736..3338886_POSITIVE 322 378 333 70 23 tfor:TF2336|3end_conserved_hypothetical_protein_2498159..2498309_POSITIVE 322 360 325 42 4 tfor:TF1818|3end_conserved_hypothetical_protein_1958754..1958904_POSITIVE 318 260 219 142 109 tfor:TF2639|3end_hypothetical_protein_2809333..2809483_POSITIVE 316 363 327 76 42 tfor:TF3072|3end_conserved_hypothetical_protein_3296083..3296233_POSITIVE 312 276 234 39 3 tfor:TF0813|3end_glycosyl_hydrolase,_secreted_872181..872331_POSITIVE 310 355 327 149 119 tfor:TF0815|3end_conserved_hypothetical_protein_873974..874124_POSITIVE 309 368 321 121 79 tfor:TF1294|3end_conserved_hypothetical_protein_1378331..1378481_POSITIVE 306 414 373 95 55 tfor:TF2882|3end_conserved_hypothetical_protein_3074401..3074551_POSITIVE 306 363 324 145 109 tfor:TF0246|3end_saccharopine_dehydrogenase_277530..277680_POSITIVE 305 367 321 52 5 tfor:TF1627|3end_guanylate_kinase_1740704..1740854_POSITIVE 304 248 208 100 59 tfor:TF1069|3end_glucokinase_regulatory_protein,_sugar_phosphate_isomerase_domain_1139794..1139944_POSITIVE 299 367 326 90 44 tfor:TF2224|3end_CTn_excision_protein_2394968..2395118_POSITIVE 298 360 336 46 12 tfor:TF1664|3end_conserved_hypothetical_protein_1779206..1779356_POSITIVE