Origin IGS: ctgctctcacttctttcctccggtttttgtgcggacaaaggtagtaataatgatggaaaaacaaccggtaaaaaatagaaacagtttcttatctttgtcggtcgaaaaccgtatataag .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 cttatatacggttttcgaccgacaaagataagaaactgtttctattttttaccggttgtttttccatcattattactacctttgtccgcacaaaaaccggaggaaagaagtgagagcag Mask Tandem Repeat Region ================================================ ctgctctcacttctttcctccggtttttgtgcggacaaaggtagtaataatgatggaaaaacaaccggtaaaaaatagaaacagtttcttatctttgtcggtcgaaaaccgtatataag Find is-nt database================================================ Query_seq: TF1601:TF1602|TF1601:TF1602:conserved hypothetical protein:L-aspartate oxidase:->->:1715600..1715718 119 ctgctctcacttctttcctccggtttttgtgcggacaaaggtagtaataatgatggaaaaacaaccggtaaaaaatagaaacagtttcttatctttgtcggtcgaaaaccgtatataag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF1601:TF1602|TF1601:TF1602:conserved hypothetical protein:L-aspartate oxidase:->->:1715600..1715718 119 ctgctctcacttctttcctccggtttttgtgcggacaaaggtagtaataatgatggaaaaacaaccggtaaaaaatagaaacagtttcttatctttgtcggtcgaaaaccgtatataag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF1601:TF1602|TF1601:TF1602:conserved hypothetical protein:L-aspartate oxidase:->->:1715600..1715718 119 ctgctctcacttctttcctccggtttttgtgcggacaaaggtagtaataatgatggaaaaacaaccggtaaaaaatagaaacagtttcttatctttgtcggtcgaaaaccgtatataag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ctgctctcacttctttcctccggtttttgtgcggacaaaggtagtaataatgatggaaaaacaaccggtaaaaaatagaaacagtttcttatctttgtcggtcgaaaaccgtatataag Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: + Start: 29 End: 115 ............................ M R T K V V I M M E K Q P V K N R N S F L S L S V E N R I * .... Protein_Len: 35 Strand: - Start: 10 End: 114 ......... K K G G T K T R V F T T I I I S F C G T F F L F L K K D K D T S F R M ..... Protein_Len: 38 Strand: - Start: 3 End: 116 .. S E S R E E P K Q A S L P L L L S P F V V P L F Y F C N R I K T P R F G Y M ... ctgctctcacttctttcctccggtttttgtgcggacaaaggtagtaataatgatggaaaaacaaccggtaaaaaatagaaacagtttcttatctttgtcggtcgaaaaccgtatataag 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================================================ ctgctctcacttctttcctccggtttttgtgcggacaaaggtagtaataatgatggaaaaacaaccggtaaaaaatagaaacagtttcttatctttgtcggtcgaaaaccgtatataag Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TF1601:TF1602|TF1601:TF1602:conserved hypothetical protein:L-aspartate oxidase:->->:1715600..1715718 119 ctgctctcacttctttcctccggtttttgtgcggacaaaggtagtaataatgatggaaaaacaaccggtaaaaaatagaaacagtttcttatctttgtcggtcgaaaaccgtatataag Intra-Species Hit: Count: 1 Min: 1 Max: 119 Len: 119 Subject: tfor_TF1601_TF1602|conserved hypothetical protein:L-aspartate oxidase|POSITIVE:POSITIVE|[1715600,1715718]|119 HSP 1 e-value: 1.0E-61 bit: 236.0 Len: 119 Query Start:1 Query End:119 Subject Strand: POSITIVE Subject Start: 1 Subject End: 119 ctgctctcacttctttcctccggtttttgtgcggacaaaggtagtaataatgatggaaaaacaaccggtaaaaaatagaaacagtttcttatctttgtcggtcgaaaaccgtatataag ctgctctcacttctttcctccggtttttgtgcggacaaaggtagtaataatgatggaaaaacaaccggtaaaaaatagaaacagtttcttatctttgtcggtcgaaaaccgtatataag Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUGCUCUCACUUCUUUCCUCCGGUUUUUGUGCGGACAAAGGUAGUAAUAAUGAUGGAAAAACAACCGGUAAAAAAUAGAAACAGUUUCUUAUCUUUGUCGGUCGAAAACCGUAUAUAAG ....................(((((((((.((.((((((((((..........(((........))).........((((.....)))))))))))))).)))))))))))........ (-26.90) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUUAUAUACGGUUUUCGACCGACAAAGAUAAGAAACUGUUUCUAUUUUUUACCGGUUGUUUUUCCAUCAUUAUUACUACCUUUGUCCGCACAAAAACCGGAGGAAAGAAGUGAGAGCAG .........((....((((((..(((((((.(((.....))))))))))...)))))).....)).......(((((.(.(((.((((.........)))).))).).)))))...... (-23.80) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 401 45 2 140 83 tfor:TF2189|5end_conserved_hypothetical_protein_2363455..2363685_POSITIVE 356 47 1 160 111 tfor:TF2271|5end_conserved_hypothetical_protein_2435802..2436032_POSITIVE 324 44 1 40 2 tfor:TF1259|5end_hypothetical_protein_1338549..1338779_POSITIVE 317 46 1 46 3 tfor:TF2267|5end_lysozyme-related_protein_2434869..2435099_POSITIVE 313 47 3 54 1 tfor:TF0287|5end_peptidase,_M23_family_315810..316040_POSITIVE 312 44 1 47 11 tfor:TF2818|5end_acetylornithine_aminotransferase_3007739..3007969_POSITIVE 306 41 5 62 13 tfor:TF0542|5end_hypothetical_protein_571918..572148_POSITIVE 302 70 21 93 50 tfor:TF0230|5end_hydrolase,_haloacid_dehalogenase-like_family_256982..257212_POSITIVE 294 38 1 174 142 tfor:TF3018|5end_polyphosphate_kinase_3240122..3240352_POSITIVE 292 38 4 136 102 tfor:TF2659|5end_conserved_hypothetical_protein_2832526..2832756_POSITIVE 289 46 3 188 144 tfor:TF2567|5end_30S_ribosomal_protein_S14_2740867..2741097_POSITIVE 289 56 12 100 61 tfor:TF2010|5end_hypothetical_protein_2163246..2163476_POSITIVE 287 40 6 187 151 tfor:TF0053|5end_hypothetical_protein_57488..57718_POSITIVE 285 43 5 100 65 tfor:TF2734|5end_conserved_hypothetical_protein_2916041..2916271_POSITIVE 285 56 11 100 65 tfor:TF1505|5end_conserved_hypothetical_protein_1610773..1611003_POSITIVE 284 45 1 156 113 tfor:TF1672|5end_ATP_synthase,_B_subunit_1786726..1786956_POSITIVE 282 46 2 96 54 tfor:TF2544|5end_cytidine_deaminase_2728322..2728552_POSITIVE 281 109 65 172 120 tfor:TF3067|5end_conserved_hypothetical_protein_3292432..3292662_POSITIVE 280 41 7 225 190 tfor:TF0504|5end_Fe-S_oxidoreductase,_family_2_528433..528663_POSITIVE 279 43 1 57 13 tfor:TF2211|5end_conserved_hypothetical_protein_2384392..2384622_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 401 45 2 140 83 tfor:TF2188|3end_conserved_hypothetical_protein_2363535..2363685_POSITIVE 317 46 1 46 3 tfor:TF2266|3end_transfer_region-related_protein,_TraQ_2434949..2435099_POSITIVE 291 47 1 85 35 tfor:TF1608|3end_sulfate_transporter_1728463..1728613_POSITIVE 284 45 1 85 42 tfor:TF1671|3end_ATP_synthase,_delta_subunit_1786735..1786885_POSITIVE 281 109 65 72 20 tfor:TF3065|3end_enolase_3292412..3292562_POSITIVE 277 42 3 58 21 tfor:TF0264|3end_ISPg3_(IS195)_transposase_293159..293309_POSITIVE 274 45 1 88 30 tfor:TF2280|3end_hypothetical_protein_2439474..2439624_POSITIVE 273 40 1 130 72 tfor:TF0086|3end_ABC_transporter,_ATP-binding_protein_93254..93404_POSITIVE 272 46 20 139 113 tfor:TF3001|3end_transposase_3217692..3217842_POSITIVE 272 46 20 139 113 tfor:TF2825|3end_transposase_3017669..3017819_POSITIVE 272 46 20 139 113 tfor:TF2591|3end_transposase_2758920..2759070_POSITIVE 272 46 20 139 113 tfor:TF0716|3end_transposase_767576..767726_POSITIVE 271 42 5 103 66 tfor:TF2553|3end_50S_ribosomal_protein_L4_2736086..2736236_POSITIVE 269 70 21 120 73 tfor:TF2477|3end_phosphatase_2654965..2655115_POSITIVE 267 68 32 107 71 tfor:TF1235|3end_L-rhamnose/H+_symporter_1320795..1320945_POSITIVE 267 42 3 115 81 tfor:TF0851|3end_helicase_SNF2_family_903168..903318_POSITIVE 265 42 1 66 27 tfor:TF3109|3end_hypothetical_protein_3342803..3342953_POSITIVE 265 47 11 137 98 tfor:TF1727|3end_hypothetical_protein_1852588..1852738_POSITIVE 264 58 19 58 14 tfor:TF0640|3end_outer_membrane_protein,_TonB_dependent_receptor_681313..681463_POSITIVE 263 42 1 105 60 tfor:TF2366|3end_conserved_hypothetical_protein_2531892..2532042_POSITIVE