Origin IGS: ggccgacgctctgttttctgtcccctcctctgcgtgttcttagccacaattttactatcttggaggaaaaaaattcataaaaataattatgaacagaaggggaaattgagcaggaatgtaaagaatccaacaaaatacgttttagaggaaaggtagttaaaaaagaacgaagatgaggaagaggcggcggaaattta .........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 taaatttccgccgcctcttcctcatcttcgttcttttttaactacctttcctctaaaacgtattttgttggattctttacattcctgctcaatttccccttctgttcataattatttttatgaatttttttcctccaagatagtaaaattgtggctaagaacacgcagaggaggggacagaaaacagagcgtcggcc Mask Tandem Repeat Region ================================================ ggccgacgctctgttttctgtcccctcctctgcgtgttcttagccacaattttactatcttggaggaaaaaaattcataaaaataattatgaacagaaggggaaattgagcaggaatgtaaagaatccaacaaaatacgttttagaggaaaggtagttaaaaaagaacgaagatgaggaagaggcggcggaaattta Find is-nt database================================================ Query_seq: TF1933:TF1935|TF1933:TF1935:methionyl-tRNA synthetase:ATP-dependent RNA helicase, DEAD/DEAH-related helicase:->->:2081945..2082141 197 ggccgacgctctgttttctgtcccctcctctgcgtgttcttagccacaattttactatcttggaggaaaaaaattcataaaaataattatgaacagaaggggaaattgagcaggaatgtaaagaatccaacaaaatacgttttagaggaaaggtagttaaaaaagaacgaagatgaggaagaggcggcggaaattta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF1933:TF1935|TF1933:TF1935:methionyl-tRNA synthetase:ATP-dependent RNA helicase, DEAD/DEAH-related helicase:->->:2081945..2082141 197 ggccgacgctctgttttctgtcccctcctctgcgtgttcttagccacaattttactatcttggaggaaaaaaattcataaaaataattatgaacagaaggggaaattgagcaggaatgtaaagaatccaacaaaatacgttttagaggaaaggtagttaaaaaagaacgaagatgaggaagaggcggcggaaattta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF1933:TF1935|TF1933:TF1935:methionyl-tRNA synthetase:ATP-dependent RNA helicase, DEAD/DEAH-related helicase:->->:2081945..2082141 197 ggccgacgctctgttttctgtcccctcctctgcgtgttcttagccacaattttactatcttggaggaaaaaaattcataaaaataattatgaacagaaggggaaattgagcaggaatgtaaagaatccaacaaaatacgttttagaggaaaggtagttaaaaaagaacgaagatgaggaagaggcggcggaaattta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ggccgacgctctgttttctgtcccctcctctgcgtgttcttagccacaattttactatcttggaggaaaaaaattcataaaaataattatgaacagaaggggaaattgagcaggaatgtaaagaatccaacaaaatacgttttagaggaaaggtagttaaaaaagaacgaagatgaggaagaggcggcggaaattta Predict ORF larger than 30AA ================================================ Protein_Len: 40 Strand: + Start: 34 End: 153 ................................. M F L A T I L L S W R K K I H K N N Y E Q K G K L S R N V K N P T K Y V L E E R ............................................ Protein_Len: 35 Strand: - Start: 90 End: 194 ......................................................................................... S C F P F N L L F T F F G V F Y T K S S L Y N F F F S S S S S A A S M ... Protein_Len: 45 Strand: - Start: 2 End: 136 . G V S Q K R D G G R R T R L W L K V I K S S F F E Y F Y N H V S P S I S C S H L S D L L M ............................................................. ggccgacgctctgttttctgtcccctcctctgcgtgttcttagccacaattttactatcttggaggaaaaaaattcataaaaataattatgaacagaaggggaaattgagcaggaatgtaaagaatccaacaaaatacgttttagaggaaaggtagttaaaaaagaacgaagatgaggaagaggcggcggaaattta 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================================================ ggccgacgctctgttttctgtcccctcctctgcgtgttcttagccacaattttactatcttggaggaaaaaaattcataaaaataattatgaacagaaggggaaattgagcaggaatgtaaagaatccaacaaaatacgttttagaggaaaggtagttaaaaaagaacgaagatgaggaagaggcggcggaaattta Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 83 HP_score: -3.7 Tail_Score: -5.52384 Start: 74 End: 93 Full_Region: caatttccccttctg ttcataa ttattt ttatgaa tttttttcctccaag .........................................................................ttcataattatttttatgaa........................................................................................................ Find igs database================================================ Query_seq: TF1933:TF1935|TF1933:TF1935:methionyl-tRNA synthetase:ATP-dependent RNA helicase, DEAD/DEAH-related helicase:->->:2081945..2082141 197 ggccgacgctctgttttctgtcccctcctctgcgtgttcttagccacaattttactatcttggaggaaaaaaattcataaaaataattatgaacagaaggggaaattgagcaggaatgtaaagaatccaacaaaatacgttttagaggaaaggtagttaaaaaagaacgaagatgaggaagaggcggcggaaattta Intra-Species Hit: Count: 1 Min: 1 Max: 197 Len: 197 Subject: tfor_TF1933_TF1935|methionyl-tRNA synthetase:ATP-dependent RNA helicase, DEAD/DEAH-related helicase|POSITIVE:POSITIVE|[2081945,2082141]|197 HSP 1 e-value: 2.0E-95 bit: 349.0 Len: 197 Query Start:1 Query End:197 Subject Strand: POSITIVE Subject Start: 1 Subject End: 197 ggccgacgctctgttttctgtcccctcctctgcgtgttcttagccacaattttactatcttggaggnnnnnnnttcataaaaataattatgaacagaaggggaaattgagcaggaatgtaaagaatccaacaaaatacgttttagaggaaaggtagttaaaaaagaacgaagatgaggaagaggcggcggaaattta ggccgacgctctgttttctgtcccctcctctgcgtgttcttagccacaattttactatcttggaggaaaaaaattcataaaaataattatgaacagaaggggaaattgagcaggaatgtaaagaatccaacaaaatacgttttagaggaaaggtagttaaaaaagaacgaagatgaggaagaggcggcggaaattta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GGCCGACGCUCUGUUUUCUGUCCCCUCCUCUGCGUGUUCUUAGCCACAAUUUUACUAUCUUGGAGGAAAAAAAUUCAUAAAAAUAAUUAUGAACAGAAGGGGAAAUUGAGCAGGAAUGUAAAGAAUCCAACAAAAUACGUUUUAGAGGAAAGGUAGUUAAAAAAGAACGAAGAUGAGGAAGAGGCGGCGGAAAUUUA ..(((.(((.((.(((..((((.(((((((((((((((....((..((((((..((.(((....)))......(((((((......))))))).....))..)))))).)).(((..........))).....)))))))...))))))..))..(((.......)))...))))..))).))))).)))....... (-43.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAAUUUCCGCCGCCUCUUCCUCAUCUUCGUUCUUUUUUAACUACCUUUCCUCUAAAACGUAUUUUGUUGGAUUCUUUACAUUCCUGCUCAAUUUCCCCUUCUGUUCAUAAUUAUUUUUAUGAAUUUUUUUCCUCCAAGAUAGUAAAAUUGUGGCUAAGAACACGCAGAGGAGGGGACAGAAAACAGAGCGUCGGCC .........((((...............((((((.((((.....((((((((((....(((.((((...(((..........))).(((((((((..(..(((((((((((......))))))))............)))..)..)))))).)))..)))).))).))))))))))....)))).)))))).)))). (-44.59) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 1057 50 1 141 92 tfor:TF2111|5end_RNA_polymerase_sigma-54_factor_2280506..2280736_POSITIVE 1057 50 1 210 161 tfor:TF0717|5end_signal_recognition_particle_767654..767884_POSITIVE 983 50 1 196 147 tfor:TF3002|5end_helicase-related_protein_3217756..3217986_POSITIVE 458 50 1 58 7 tfor:TF1145|5end_anaerobic_C4-dicarboxylate_membrane_transporter_1225799..1226029_POSITIVE 381 46 2 211 175 tfor:TF2259|5end_transfer_region-related_protein,_TraK_2429577..2429807_POSITIVE 379 36 6 161 121 tfor:TF2616|5end_outer_membrane_protein,_TonB_dependent_receptor_2791470..2791700_POSITIVE 350 46 1 59 5 tfor:TF2317|5end_3-oxoacyl-[acyl-carrier-protein]_synthase_II_2474418..2474648_POSITIVE 342 45 1 184 131 tfor:TF2348|5end_outer_membrane_protein,_possibly_involved_in_nutrient_binding_2511088..2511318_POSITIVE 339 47 1 230 175 tfor:TF0815|5end_conserved_hypothetical_protein_873199..873429_POSITIVE 337 31 3 230 205 tfor:TF0830|5end_hypothetical_protein_887610..887840_POSITIVE 335 41 1 69 20 tfor:TF2704|5end_ribonuclease_HII_2876242..2876472_POSITIVE 329 45 1 217 164 tfor:TF1767|5end_3-dehydroquinate_synthase_1905492..1905722_POSITIVE 327 190 150 208 162 tfor:TF1634|5end_hypothetical_protein_1746831..1747061_POSITIVE 322 44 1 53 1 tfor:TF1942|5end_conserved_hypothetical_protein_2090129..2090359_POSITIVE 320 34 1 147 108 tfor:TF1250|5end_possible_cation_efflux_pump_1332324..1332554_POSITIVE 319 45 1 212 169 tfor:TF2560|5end_30S_ribosomal_protein_S3_2737897..2738127_POSITIVE 319 45 1 140 98 tfor:TF1253|5end_hypothetical_protein_1335982..1336212_POSITIVE 318 47 1 130 77 tfor:TF2189|5end_conserved_hypothetical_protein_2363455..2363685_POSITIVE 317 64 24 72 28 tfor:TF2793|5end_possible_L-lysine_2,3-aminomutase_2977661..2977891_POSITIVE 315 45 3 98 54 tfor:TF2312|5end_conserved_hypothetical_protein;_possible_glycosyl_transferase_2471537..2471767_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 1057 50 1 81 32 tfor:TF2110|3end_transposase_2280526..2280676_POSITIVE 1057 50 1 52 3 tfor:TF0716|3end_transposase_767576..767726_POSITIVE 983 50 1 52 3 tfor:TF3001|3end_transposase_3217692..3217842_POSITIVE 983 50 1 52 3 tfor:TF2825|3end_transposase_3017669..3017819_POSITIVE 983 50 1 52 3 tfor:TF2591|3end_transposase_2758920..2759070_POSITIVE 510 179 131 67 8 tfor:TF2109|3end_possible_metallo-beta-lactamase_family_protein_2278960..2279110_POSITIVE 350 46 1 59 5 tfor:TF2315|3end_thioesterase_2474498..2474648_POSITIVE 342 45 1 108 55 tfor:TF2347|3end_outer_membrane_protein,_TonB_dependent_receptor_2511092..2511242_POSITIVE 337 31 3 48 23 tfor:TF0828|3end_hypothetical_protein_887508..887658_POSITIVE 335 41 1 64 15 tfor:TF2703|3end_conserved_hypothetical_protein_2876317..2876467_POSITIVE 327 190 150 128 82 tfor:TF1635|3end_conserved_hypothetical_protein;_possible_helicase_1746831..1746981_POSITIVE 320 34 1 99 60 tfor:TF1249|3end_phosphoglycerate_kinase_(cytosolic_phosphoglycerate_kinase)_1332356..1332506_POSITIVE 318 47 1 130 77 tfor:TF2188|3end_conserved_hypothetical_protein_2363535..2363685_POSITIVE 315 45 3 93 49 tfor:TF2311|3end_conserved_hypothetical_protein_2471612..2471762_POSITIVE 311 35 1 52 17 tfor:TF3009|3end_RNA_polymerase_ECF-type_sigma_factor_3229709..3229859_POSITIVE 311 50 1 92 36 tfor:TF2171|3end_hypothetical_protein_2345792..2345942_POSITIVE 311 45 2 74 21 tfor:TF0010|3end_conserved_hypothetical_protein_4790..4940_POSITIVE 303 47 8 40 1 tfor:TF2266|3end_transfer_region-related_protein,_TraQ_2434949..2435099_POSITIVE 297 45 2 97 50 tfor:TF2640|3end_hypothetical_protein_2809533..2809683_POSITIVE 297 44 1 142 91 tfor:TF1832|3end_3-isopropylmalate_dehydratase,_small_subunit_1981502..1981652_POSITIVE